BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716645.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 = 1,116,911 number of mapped reads = 1,005,834 (90.05%) number of supplementary alignments = 3,075 (0.28%) number of secondary alignments = 0 number of mapped bases = 57,522,848 bp number of sequenced bases = 57,505,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,086 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1372 >>>>>>> ACTG content number of A's = 14,340,336 bp (24.94%) number of C's = 10,458,822 bp (18.19%) number of T's = 18,854,606 bp (32.79%) number of G's = 13,850,724 bp (24.09%) number of N's = 1,049 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 300,156 number of insertions = 3,820 mapped reads with insertion percentage = 0.38% number of deletions = 10,815 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.1972X There is a 1.72% 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 4856694 0.019485183148249808 0.2755836258198918 chr2 243199373 4505511 0.018525997597863872 0.3123839697474969 chr3 198022430 3288280 0.016605593618864288 0.13722246727317036 chr4 191154276 3539231 0.018515050115855112 0.16251599888462545 chr5 180915260 3330315 0.018408148654790093 0.14382510648278177 chr6 171115067 3053897 0.017847037397355547 0.16206936887845866 chr7 159138663 3286410 0.020651235457470194 0.23763901537786797 chr8 146364022 3012400 0.020581560678894162 0.2314117871771488 chr9 141213431 1922968 0.013617458243047716 0.14668398491265494 chr10 135534747 2561461 0.018898924863894866 0.20576086907791266 chr11 135006516 2045448 0.015150735391171786 0.15548923542580492 chr12 133851895 2848475 0.0212807969584592 0.15519604565949371 chr13 115169878 1737113 0.015083049753686463 0.1301099945264241 chr14 107349540 1935213 0.01802721278544836 0.14355764686429964 chr15 102531392 2121826 0.020694403524727335 0.15396289625440485 chr16 90354753 1968059 0.021781466216835323 0.1624695914882968 chr17 81195210 2479747 0.030540557749650504 0.19057273060980431 chr18 78077248 1102581 0.01412166832519507 0.21445309536896065 chr19 59128983 1465398 0.02478307465562193 0.2402441576739416 chr20 63025520 1859516 0.029504175451467912 0.1870077220828261 chr21 48129895 728368 0.015133380199562039 0.14905054650235422 chr22 51304566 538122 0.010488774040111752 0.10849591351462924 chrMT 16571 42862 2.586566893971396 2.202631292628937 chrX 155270560 3079103 0.01983056543365336 0.15869374163662497 chrY 59373566 213850 0.0036017711989877787 0.16442172195233604