BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716106.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 = 1,446,436 number of mapped reads = 1,164,131 (80.48%) number of supplementary alignments = 5,521 (0.38%) number of secondary alignments = 0 number of mapped bases = 67,165,554 bp number of sequenced bases = 67,145,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,220 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6126 >>>>>>> ACTG content number of A's = 17,194,061 bp (25.61%) number of C's = 11,353,113 bp (16.91%) number of T's = 21,664,673 bp (32.27%) number of G's = 16,931,964 bp (25.22%) number of N's = 1,854 bp (0%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 338,901 number of insertions = 4,692 mapped reads with insertion percentage = 0.4% number of deletions = 12,772 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0217X std coverageData = 0.2123X There is a 1.99% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 7665019 0.03075225638053676 0.35072872262498517 chr2 243199373 5895492 0.024241394734187904 0.2757378221376307 chr3 198022430 4793066 0.024204662067827367 0.16685658379963553 chr4 191154276 3183027 0.0166516128574597 0.14372743311412164 chr5 180915260 3036618 0.016784753259620002 0.14019671356755167 chr6 171115067 5838102 0.03411798915404685 0.2380616979347033 chr7 159138663 3921919 0.02464466476006525 0.25702228581244907 chr8 146364022 4855765 0.03317594675008316 0.21715735826315047 chr9 141213431 2859716 0.020251019890593833 0.19861890831793286 chr10 135534747 3445084 0.025418455977196754 0.24277132206170352 chr11 135006516 2268980 0.01680644806803251 0.1710001506086632 chr12 133851895 3037324 0.022691677245211955 0.16520324055836363 chr13 115169878 1554895 0.013500882583204612 0.12453269266437501 chr14 107349540 1497066 0.013945714159557646 0.13861601741942456 chr15 102531392 2014938 0.01965191304532372 0.1522320434065139 chr16 90354753 1452555 0.016076132707706036 0.15300290204832692 chr17 81195210 1544872 0.019026639625662648 0.15280453091559934 chr18 78077248 1349869 0.017288890612537983 0.31050947910342386 chr19 59128983 1265598 0.021404021104168156 0.2405279993709074 chr20 63025520 1172545 0.01860428918317532 0.1473776106992912 chr21 48129895 628773 0.0130640841830218 0.13349720198400278 chr22 51304566 835477 0.016284651935268294 0.13645165885826205 chrMT 16571 1672 0.10089916118520306 0.3533759700621821 chrX 155270560 2890196 0.01861393428348555 0.16496351416022204 chrY 59373566 156986 0.0026440385945489613 0.07246701946122291