BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716266.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,590,429 number of mapped reads = 883,274 (55.54%) number of supplementary alignments = 932 (0.06%) number of secondary alignments = 0 number of mapped bases = 43,186,459 bp number of sequenced bases = 43,176,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,499 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7666 >>>>>>> ACTG content number of A's = 8,817,243 bp (20.42%) number of C's = 6,136,962 bp (14.21%) number of T's = 14,948,025 bp (34.62%) number of G's = 13,273,893 bp (30.74%) number of N's = 667 bp (0%) GC percentage = 44.96% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 347,799 number of insertions = 2,552 mapped reads with insertion percentage = 0.29% number of deletions = 6,032 mapped reads with deletion percentage = 0.68% homopolymer indels = 39.96% >>>>>>> Coverage mean coverageData = 0.014X std coverageData = 0.156X There is a 1.3% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% 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 3537517 0.014192610577287188 0.14309517432573782 chr2 243199373 3498599 0.014385723765825663 0.29042329675327794 chr3 198022430 2748771 0.013881109326857568 0.12652828408136657 chr4 191154276 2667545 0.01395493240234919 0.14095967324729683 chr5 180915260 2608232 0.014416871191518061 0.12788982278409208 chr6 171115067 2330207 0.013617778030031686 0.17206466803681464 chr7 159138663 2323639 0.014601348008057602 0.14410809670143507 chr8 146364022 2131874 0.014565560380678797 0.13356014181995718 chr9 141213431 1790048 0.01267618800367509 0.13181415977431182 chr10 135534747 2045573 0.015092609425094512 0.161709764821156 chr11 135006516 1927669 0.01427834046173001 0.13877501237403705 chr12 133851895 2027008 0.01514366307626799 0.1323928885870218 chr13 115169878 1230005 0.010679919275420263 0.11431752281837887 chr14 107349540 1372790 0.01278803802978569 0.1225590304558124 chr15 102531392 1291678 0.012597878316135609 0.12242183282573733 chr16 90354753 1377806 0.0152488491667948 0.1453288104302125 chr17 81195210 1373974 0.01692186029200491 0.1404992365770729 chr18 78077248 1087148 0.01392400510837677 0.14853357720452023 chr19 59128983 1100648 0.01861435702352601 0.15899392939532342 chr20 63025520 977061 0.015502624968425489 0.13560163370532113 chr21 48129895 577989 0.012008939558251686 0.1276512936144409 chr22 51304566 598446 0.01166457581962588 0.11559982426113939 chrMT 16571 53058 3.2018586687586748 3.1720428436268793 chrX 155270560 2312867 0.014895721378218768 0.13627520417638458 chrY 59373566 196307 0.0033063030103329147 0.10171283818713309