BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716097.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 = 718,394 number of mapped reads = 662,192 (92.18%) number of supplementary alignments = 10,212 (1.42%) number of secondary alignments = 0 number of mapped bases = 52,334,402 bp number of sequenced bases = 52,312,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,263 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6407 >>>>>>> ACTG content number of A's = 12,933,018 bp (24.72%) number of C's = 10,383,193 bp (19.85%) number of T's = 16,037,284 bp (30.66%) number of G's = 12,956,619 bp (24.77%) number of N's = 2,860 bp (0.01%) GC percentage = 44.62% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 419,857 number of insertions = 5,145 mapped reads with insertion percentage = 0.77% number of deletions = 12,395 mapped reads with deletion percentage = 1.85% homopolymer indels = 43.52% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.2096X There is a 1.56% of reference with a coverageData >= 1X There is a 0.09% 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 4308513 0.01728586666189289 0.3075938343694306 chr2 243199373 4439331 0.018253875185771963 0.2953619465177444 chr3 198022430 3387923 0.01710878409077194 0.13867799592821006 chr4 191154276 3207408 0.016779159049520816 0.14267353606261543 chr5 180915260 3103126 0.017152372884410082 0.140426511236953 chr6 171115067 2995810 0.017507575764792237 0.1545149040616696 chr7 159138663 2849403 0.017905158597442784 0.25335314647451407 chr8 146364022 2562007 0.01750434953201819 0.27766441563397215 chr9 141213431 2182560 0.015455753638618128 0.2209545228429509 chr10 135534747 2463804 0.01817839376643393 0.19559923642138086 chr11 135006516 2359905 0.0174799340796262 0.20040731949718676 chr12 133851895 2473489 0.018479297584841813 0.1457180369709044 chr13 115169878 1558355 0.013530925160830681 0.12201247842711523 chr14 107349540 1622326 0.015112556607135903 0.14705122289176864 chr15 102531392 1536523 0.014985878666311288 0.13097429311054395 chr16 90354753 1630241 0.01804267009617081 0.1516207453127986 chr17 81195210 1606644 0.0197874234206673 0.155984621577013 chr18 78077248 1366899 0.01750700793142709 0.3958126768466614 chr19 59128983 1245110 0.021057524361614677 0.2602090220586415 chr20 63025520 1112781 0.01765603837937394 0.14713484008445546 chr21 48129895 678280 0.014092696441577526 0.13036353116901497 chr22 51304566 677682 0.013208999760372205 0.12234207330401937 chrMT 16571 16280 0.9824392010138193 1.1750646538782368 chrX 155270560 2820022 0.018161987694254467 0.17199211173860332 chrY 59373566 129980 0.0021891897144934837 0.06974105404488054