BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173978.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 = 2,776,332 number of mapped reads = 2,721,795 (98.04%) number of supplementary alignments = 323,146 (11.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,361,319 number of mapped paired reads (second in pair) = 1,360,476 number of mapped paired reads (both in pair) = 2,691,208 number of mapped paired reads (singletons) = 30,587 number of mapped bases = 307,473,324 bp number of sequenced bases = 307,266,582 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,104,609 duplication rate = 62.36% >>>>>>> Insert size mean insert size = 876,067.3663 std insert size = 8,723,971.9458 median insert size = 145 >>>>>>> Mapping quality mean mapping quality = 52.7859 >>>>>>> ACTG content number of A's = 92,442,035 bp (30.09%) number of C's = 60,707,960 bp (19.76%) number of T's = 91,505,626 bp (29.78%) number of G's = 62,608,430 bp (20.38%) number of N's = 2,531 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,578,989 number of insertions = 32,421 mapped reads with insertion percentage = 1.15% number of deletions = 86,864 mapped reads with deletion percentage = 3.11% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0993X std coverageData = 1.7743X There is a 2.27% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.94% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.59% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% 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 24569814 0.09857473534639659 1.120413127997211 chr2 243199373 28217517 0.11602627363681567 5.239070014666274 chr3 198022430 21255717 0.10733994628790285 0.986261749339714 chr4 191154276 21130827 0.11054331319274281 1.117967042118533 chr5 180915260 18993371 0.10498490287662854 0.9644982523635701 chr6 171115067 18542254 0.10836131689093165 1.0510645995459262 chr7 159138663 14977111 0.09411359073690345 1.0170098067058655 chr8 146364022 15875060 0.10846285708109334 1.3505168854126897 chr9 141213431 12773405 0.09045460413747755 0.9911487202389851 chr10 135534747 15082228 0.11127941973433572 1.3100623754578773 chr11 135006516 14554602 0.10780666319838962 0.9866799868795542 chr12 133851895 14448953 0.10794731744365667 0.995120631512035 chr13 115169878 10056103 0.08731539161654751 0.8779558057789532 chr14 107349540 10078848 0.0938881340339232 0.9173197542206315 chr15 102531392 8353663 0.08147419865322808 0.8458963429302881 chr16 90354753 9453006 0.10462101534381926 1.0745817501296657 chr17 81195210 8910854 0.10974605521680404 1.0074387219393877 chr18 78077248 8904204 0.1140435175174207 1.3415430646839752 chr19 59128983 5788946 0.09790369639876945 0.9967603154571809 chr20 63025520 6908352 0.10961197940135996 1.0065481547559432 chr21 48129895 4376480 0.09093059521530225 1.0486915460525765 chr22 51304566 3755507 0.07320024888233145 0.846665811292375 chrMT 16571 320445 19.337698388751434 19.793514816438844 chrX 155270560 7781641 0.05011665443854907 0.665041681560779 chrY 59373566 2364416 0.039822704939096974 0.67777675672497