BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717019.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 = 2,141,702 number of mapped reads = 2,038,393 (95.18%) number of supplementary alignments = 40,224 (1.88%) number of secondary alignments = 0 number of mapped bases = 160,528,050 bp number of sequenced bases = 160,465,003 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,079 duplication rate = 4.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6018 >>>>>>> ACTG content number of A's = 39,472,202 bp (24.6%) number of C's = 33,700,742 bp (21%) number of T's = 47,384,644 bp (29.53%) number of G's = 39,901,239 bp (24.87%) number of N's = 6,176 bp (0%) GC percentage = 45.87% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,017,420 number of insertions = 13,957 mapped reads with insertion percentage = 0.67% number of deletions = 30,126 mapped reads with deletion percentage = 1.45% homopolymer indels = 38.54% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.4345X There is a 4.11% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 18158471 0.07285225981442991 0.868157423731161 chr2 243199373 14774908 0.060752245442672256 0.4249227073494883 chr3 198022430 9936965 0.05018100727276198 0.27452096825742023 chr4 191154276 9336225 0.048841308681998825 0.40290972447259155 chr5 180915260 9065454 0.05010884101208488 0.2747401119893516 chr6 171115067 9262888 0.054132509558611805 0.29907963072060395 chr7 159138663 14157679 0.08896442092139482 0.6444649140532572 chr8 146364022 10139073 0.06927298704595587 0.4326750287661042 chr9 141213431 4668477 0.033059723617932635 0.2764294337938204 chr10 135534747 8595741 0.06342093957647628 0.6003776953262161 chr11 135006516 5057475 0.037460969661642106 0.3174068719707197 chr12 133851895 5234279 0.03910500482641654 0.23872760358797507 chr13 115169878 3199021 0.027776542404603397 0.1983677302347512 chr14 107349540 2899188 0.02700699043517094 0.21767753597043732 chr15 102531392 2987482 0.02913724218237474 0.20571365178551293 chr16 90354753 4725131 0.052295323080568876 0.30144273868772264 chr17 81195210 2763488 0.03403511118451446 0.2544802285977061 chr18 78077248 4569489 0.05852523131962848 0.43321880816050795 chr19 59128983 3949146 0.06678866775029768 0.6164806302386441 chr20 63025520 4197374 0.0665980066487353 0.33807447254239087 chr21 48129895 2565659 0.05330697272454054 0.35906943858137913 chr22 51304566 2488961 0.048513440304708944 0.2832508017212542 chrMT 16571 68195 4.115321947981413 3.8787962539591976 chrX 155270560 7218348 0.046488838579573616 0.2838603751250529 chrY 59373566 508933 0.00857171017822982 0.3515486197501264