BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716571.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 = 1,052,692 number of mapped reads = 989,147 (93.96%) number of supplementary alignments = 26,498 (2.52%) number of secondary alignments = 0 number of mapped bases = 76,104,962 bp number of sequenced bases = 76,074,640 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,903 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3569 >>>>>>> ACTG content number of A's = 19,100,460 bp (25.11%) number of C's = 15,869,597 bp (20.86%) number of T's = 22,409,315 bp (29.46%) number of G's = 18,692,292 bp (24.57%) number of N's = 2,976 bp (0%) GC percentage = 45.43% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 484,877 number of insertions = 6,877 mapped reads with insertion percentage = 0.68% number of deletions = 14,656 mapped reads with deletion percentage = 1.45% homopolymer indels = 38.54% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2177X There is a 2.2% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6245440 0.025056868363830476 0.2801479423351011 chr2 243199373 6332462 0.026038151011187022 0.24761323664528456 chr3 198022430 4965218 0.025074018130168386 0.1720767813638647 chr4 191154276 4794467 0.02508166231133642 0.23038735362373683 chr5 180915260 4463857 0.0246737450450559 0.17090205612926102 chr6 171115067 4297952 0.025117320615606575 0.1780005726982493 chr7 159138663 4111999 0.025839094802499376 0.2543415092215677 chr8 146364022 3783685 0.025851195862874005 0.21716437714587472 chr9 141213431 3146200 0.022279750429688234 0.1967855557144321 chr10 135534747 3749508 0.027664551585432184 0.29166745981548686 chr11 135006516 3448398 0.025542456039677374 0.22664627429264836 chr12 133851895 3460864 0.025855920829510857 0.17678238146697792 chr13 115169878 2356151 0.020458048935330122 0.15650709336532898 chr14 107349540 2286427 0.021298898905388882 0.16767817093508647 chr15 102531392 2221711 0.02166859297101906 0.16067102444833514 chr16 90354753 2370809 0.026238896364422577 0.18926997640908969 chr17 81195210 2166613 0.02668400020148972 0.19656163959787967 chr18 78077248 2050341 0.02626041583842709 0.29866058738023615 chr19 59128983 1687313 0.028536141066387022 0.24167439765627674 chr20 63025520 1764841 0.028002006171468318 0.19233735095544272 chr21 48129895 1033085 0.021464518050579584 0.1968082662088908 chr22 51304566 1023547 0.019950407532927966 0.15608378435029865 chrMT 16571 33253 2.0066984490978217 2.0447186631083394 chrX 155270560 4035361 0.025989221652836184 0.2134672504730598 chrY 59373566 275460 0.00463943836555143 0.19452942796131492