BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716610.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 = 4,041,055 number of mapped reads = 3,622,713 (89.65%) number of supplementary alignments = 96,932 (2.4%) number of secondary alignments = 0 number of mapped bases = 273,797,630 bp number of sequenced bases = 273,694,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,717 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4345 >>>>>>> ACTG content number of A's = 72,804,886 bp (26.6%) number of C's = 57,344,697 bp (20.95%) number of T's = 80,919,145 bp (29.57%) number of G's = 62,592,017 bp (22.87%) number of N's = 33,330 bp (0.01%) GC percentage = 43.82% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,080,171 number of insertions = 23,717 mapped reads with insertion percentage = 0.65% number of deletions = 58,874 mapped reads with deletion percentage = 1.6% homopolymer indels = 39.85% >>>>>>> Coverage mean coverageData = 0.0884X std coverageData = 0.6802X There is a 7.01% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 26285895 0.10545969712950083 1.1876703045382286 chr2 243199373 22293451 0.09166738682340271 1.0504631765012302 chr3 198022430 22130165 0.11175585008223564 0.4228104845510027 chr4 191154276 11340788 0.0593279325857194 0.3427698134380868 chr5 180915260 16836815 0.0930646480567753 0.38094484511980686 chr6 171115067 20672429 0.12081010376485432 0.536629529029209 chr7 159138663 13008644 0.08174408251752122 0.8981171063305556 chr8 146364022 17660226 0.12065961128070121 0.8258463039913566 chr9 141213431 14048932 0.09948722228836718 0.6238094498537221 chr10 135534747 15092755 0.11135708985386604 0.672799753117033 chr11 135006516 12304373 0.09113910472291574 0.5401852923295414 chr12 133851895 9674597 0.07227837155387304 0.3294529910935193 chr13 115169878 8360975 0.07259689030841901 0.3210054230984963 chr14 107349540 5589529 0.0520684951235003 0.3401189056624028 chr15 102531392 5455847 0.053211478880536414 0.2790909828079772 chr16 90354753 6802078 0.07528190575652395 0.3884296917473325 chr17 81195210 8202253 0.1010189271017342 0.4620851686460372 chr18 78077248 8286847 0.1061365149550353 1.1497565803649206 chr19 59128983 4843494 0.08191404205277808 0.9328871667504147 chr20 63025520 4919930 0.07806250547397309 0.3921547035177818 chr21 48129895 5774785 0.11998332844898166 0.4595434181202775 chr22 51304566 3826764 0.07458915060308667 0.3388053486324794 chrMT 16571 141462 8.53672077726148 6.219306197932686 chrX 155270560 9629385 0.06201681117141588 0.4219484648782011 chrY 59373566 615211 0.010361698672436147 0.3140100995974023