Examples
Paired-end report (2x50bp):
Input file: 'FVBNJ_Cast.bam'
Writing allele-flagged output file to: 'FVBNJ_Cast.allele_flagged.bam'
Allele-tagging report
=====================
Processed 194564995 read alignments in total
149380724 reads were unassignable (76.78%)
35143075 reads were specific for genome 1 (18.06%)
9860248 reads were specific for genome 2 (5.07%)
118662 reads did not contain one of the expected bases at known SNP positions (0.06%)
180948 contained conflicting allele-specific SNPs (0.09%)
SNP coverage report
===================
N-containing reads: 45276050
non-N: 149262062
total: 194564995
Reads had a deletion of the N-masked position (and were thus dropped): 26883 (0.01%)
Of which had multiple deletions of N-masked positions within the same read: 30
Of valid N containing reads,
N was present in the list of known SNPs: 61087551 (99.99%)
N was not present in the list of SNPs: 4773 (0.01%)
Input file: 'FVBNJ_Cast.allele_flagged.bam'
Writing unassigned reads to: 'FVBNJ_Cast.unassigned.bam'
Writing genome 1-specific reads to: 'FVBNJ_Cast.genome1.bam'
Writing genome 2-specific reads to: 'FVBNJ_Cast.genome2.bam'
Allele-specific paired-end sorting report
=========================================
Read pairs/singletons processed in total: 98215744
thereof were read pairs: 96349251
thereof were singletons: 1866493
Reads were unassignable (not overlapping SNPs): 61174812 (62.29%)
thereof were read pairs: 59662537
thereof were singletons: 1512275
Reads were specific for genome 1: 28657857 (29.18%)
thereof were read pairs: 28446094
thereof were singletons: 211763
Reads were specific for genome 2: 8122687 (8.27%)
thereof were read pairs: 7985424
thereof were singletons: 137263
Reads contained conflicting SNP information: 260388 (0.27%)
thereof were read pairs: 255196
thereof were singletons: 5192
Hi-C report (2x100bp):
Input file: Black6_129S1.bam
Writing allele-flagged output file to: Black6_129S1.allele_flagged.bam
Allele-tagging report
=====================
Processed 94887256 read alignments in total
59662038 reads were unassignable (62.88%)
19851697 reads were specific for genome 1 (20.92%)
15047281 reads were specific for genome 2 (15.86%)
47261 reads did not contain one of the expected bases at known SNP positions (0.05%)
326240 contained conflicting allele-specific SNPs (0.34%)
SNP coverage report
===================
N-containing reads: 35231977
non-N: 59614777
total: 94887256
Reads had a deletion of the N-masked position (and were thus dropped): 40502 (0.04%)
Of which had multiple deletions of N-masked positions within the same read: 59
Of valid N containing reads,
N was present in the list of known SNPs: 57101748 (99.99%)
N was not present in the list of SNPs: 4211 (0.01%)
Input file: Black6_129S1.allele_flagged.bam'
Writing unassigned reads to: Black6_129S1.UA_UA.bam'
Writing genome 1-specific reads to: Black6_129S1.G1_G1.bam'
Writing genome 2-specific reads to: Black6_129S1.G2_G2.bam'
Writing G1/UA reads to: Black6_129S1.G1_UA.bam'
Writing G2/UA reads to: Black6_129S1.G2_UA.bam'
Writing G1/G2 reads to: Black6_129S1.G1_G2.bam'
Allele-specific paired-end sorting report
=========================================
Read pairs processed in total: 47443628
Read pairs were unassignable (UA/UA): 18862725 (39.76%)
Read pairs were specific for genome 1 (G1/G1): 3533932 (7.45%)
Read pairs were specific for genome 2 (G2/G2): 2592040 (5.46%)
Read pairs were a mix of G1 and UA: 12306421 (25.94%). Of these,
were G1/UA: 6018598
were UA/G1: 6287823
Read pairs were a mix of G2 and UA: 9430675 (19.88%). Of these,
were G2/UA: 4603429
were UA/G2: 4827246
Read pairs were a mix of G1 and G2: 395296 (0.83%). Of these,
were G1/G2: 198330
were G2/G1: 196966
Read pairs contained conflicting SNP information: 322539 (0.68%)
BS-Seq report (2x100bp):
Input file: '129_Cast_bismark_bt2_pe.bam'
Writing allele-flagged output file to: '129_Cast_bismark_bt2_pe.allele_flagged.bam'
Allele-tagging report
=====================
Processed 162441396 read alignments in total
Reads were unaligned and hence skipped: 0 (0.00%)
109109113 reads were unassignable (67.17%)
30267901 reads were specific for genome 1 (18.63%)
22697499 reads were specific for genome 2 (13.97%)
15807753 reads did not contain one of the expected bases at known SNP positions (9.73%)
366883 contained conflicting allele-specific SNPs (0.23%)
SNP coverage report
===================
SNP annotation file: ../all_Cast_SNPs_129S1_reference.mgp.v4.txt.gz
N-containing reads: 68984287
non-N: 93301360
total: 162441396
Reads had a deletion of the N-masked position (and were thus dropped): 155749 (0.10%)
Of which had multiple deletions of N-masked positions within the same read: 65
Of valid N containing reads,
N was present in the list of known SNPs: 119119643 (99.99%)
Positions were skipped since they involved C>T SNPs: 38464451
N was not present in the list of SNPs: 7517 (0.01%)
Input file: 129_Cast_bismark_bt2_pe.allele_flagged.bam'
Writing unassigned reads to: 129_Cast_bismark_bt2_pe.unassigned.bam'
Writing genome 1-specific reads to: 129_Cast_bismark_bt2_pe.genome1.bam'
Writing genome 2-specific reads to: 129_Cast_bismark_bt2_pe.genome2.bam'
Allele-specific paired-end sorting report
=========================================
Read pairs/singletons processed in total: 81220698
thereof were read pairs: 81220698
thereof were singletons: 0
Reads were unassignable (not overlapping SNPs): 40420625 (49.77%)
thereof were read pairs: 40420625
thereof were singletons: 0
Reads were specific for genome 1: 23037433 (28.36%)
thereof were read pairs: 23037433
thereof were singletons: 0
Reads were specific for genome 2: 17303663 (21.30%)
thereof were read pairs: 17303663
thereof were singletons: 0
Reads contained conflicting SNP information: 458977 (0.57%)
thereof were read pairs: 458977
thereof were singletons: 0