BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716971.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 = 3,855,075 number of mapped reads = 3,347,817 (86.84%) number of supplementary alignments = 11,167 (0.29%) number of secondary alignments = 0 number of mapped bases = 189,798,008 bp number of sequenced bases = 189,739,585 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,859 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8413 >>>>>>> ACTG content number of A's = 48,563,205 bp (25.59%) number of C's = 37,182,401 bp (19.6%) number of T's = 59,635,630 bp (31.43%) number of G's = 44,355,322 bp (23.38%) number of N's = 3,027 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 978,242 number of insertions = 12,600 mapped reads with insertion percentage = 0.37% number of deletions = 37,474 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0613X std coverageData = 0.4817X There is a 5.1% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 17066621 0.06847172910353551 0.6257840910187636 chr2 243199373 18972892 0.07801373731337703 0.7227761842865168 chr3 198022430 13186054 0.06658868896821436 0.3526121583317569 chr4 191154276 11203403 0.05860921991616865 0.3006408499300468 chr5 180915260 9001638 0.04975610128189297 0.2654512124701536 chr6 171115067 10776307 0.06297696157872527 0.36091293234804844 chr7 159138663 9579106 0.06019345531387303 0.8275652290286883 chr8 146364022 13002134 0.08883422184175835 0.48814753588257515 chr9 141213431 7799050 0.05522881176932809 0.37366539771898083 chr10 135534747 9432894 0.06959760658276065 0.7605548479190494 chr11 135006516 7314592 0.05417954789678448 0.38712384086205626 chr12 133851895 10964654 0.08191631504357857 0.39102319162594473 chr13 115169878 5982706 0.05194679462975554 0.26670239837728393 chr14 107349540 6083593 0.05667088093717029 0.2942588433702054 chr15 102531392 4410381 0.04301493341668472 0.2581497624644677 chr16 90354753 5718762 0.06329232065965583 0.34750699748546876 chr17 81195210 6955577 0.0856648686541977 0.37870858158266507 chr18 78077248 4255412 0.054502586976426216 0.6066691061867311 chr19 59128983 3412164 0.057707131543256886 0.6457262943488 chr20 63025520 3705750 0.05879761087254814 0.3256902884131351 chr21 48129895 1867212 0.03879526435700722 0.24812534347906107 chr22 51304566 2574839 0.050187326406776346 0.2634311784566615 chrMT 16571 15521 0.9366362923179048 1.2100121396546495 chrX 155270560 6121258 0.03942317204240134 0.34549442579856177 chrY 59373566 395488 0.006661011400258492 0.14427656736493297