BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173977.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 5,248,898 number of mapped reads = 5,139,055 (97.91%) number of supplementary alignments = 626,402 (11.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,571,801 number of mapped paired reads (second in pair) = 2,567,254 number of mapped paired reads (both in pair) = 5,072,456 number of mapped paired reads (singletons) = 66,599 number of mapped bases = 576,502,462 bp number of sequenced bases = 576,130,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,879,752 duplication rate = 62.11% >>>>>>> Insert size mean insert size = 975,078.9614 std insert size = 8,586,963.3764 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.7049 >>>>>>> ACTG content number of A's = 173,372,063 bp (30.09%) number of C's = 113,414,833 bp (19.69%) number of T's = 171,818,974 bp (29.82%) number of G's = 117,520,109 bp (20.4%) number of N's = 4,483 bp (0%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 4,803,993 number of insertions = 65,844 mapped reads with insertion percentage = 1.23% number of deletions = 157,402 mapped reads with deletion percentage = 2.99% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.1862X std coverageData = 3.2951X There is a 4.51% of reference with a coverageData >= 1X There is a 3.24% of reference with a coverageData >= 2X There is a 2.28% of reference with a coverageData >= 3X There is a 1.8% of reference with a coverageData >= 4X There is a 1.29% of reference with a coverageData >= 5X There is a 1.07% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.67% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 48227197 0.19348877369497106 1.7721419086366261 chr2 243199373 52488312 0.21582420773757505 10.484662999959683 chr3 198022430 38385937 0.19384640921738008 1.243624544621253 chr4 191154276 38856336 0.2032721255997433 1.8656186287862218 chr5 180915260 35322865 0.1952453596230633 1.2463000317914978 chr6 171115067 35540745 0.20770085079649941 1.4450432816252554 chr7 159138663 32464479 0.20400120491146767 1.6983499039588996 chr8 146364022 30264486 0.2067754464959975 2.3895793530857548 chr9 141213431 23984504 0.16984577054855357 1.4655331120397492 chr10 135534747 29897639 0.22059021514239444 2.1383243420146982 chr11 135006516 24977426 0.18500904060067738 1.239549752541217 chr12 133851895 26749862 0.19984671864376669 1.3050632524079826 chr13 115169878 18399098 0.1597561647152218 1.1258894113446751 chr14 107349540 17729525 0.1651569722608965 1.1511115037972646 chr15 102531392 16303924 0.15901397300838363 1.1500422969777586 chr16 90354753 15842929 0.17534140124316427 1.356539761411585 chr17 81195210 15679619 0.1931101477537899 1.3069121643873312 chr18 78077248 15729317 0.20145839412782582 1.9899408001412577 chr19 59128983 10227020 0.17296120246140542 1.355716752329278 chr20 63025520 12679782 0.2011848851068583 1.373901367420084 chr21 48129895 8385613 0.1742287823399573 1.5589838714857036 chr22 51304566 6895958 0.13441216908452164 1.2621004442234622 chrMT 16571 1024702 61.83706475167461 53.64469626845539 chrX 155270560 15948812 0.10271626507948448 0.9002164161708521 chrY 59373566 4496375 0.07573025005774456 1.4628719848315284