BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238245.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,265,244 number of mapped reads = 823,242 (65.07%) number of supplementary alignments = 9,154 (0.72%) number of secondary alignments = 0 number of mapped bases = 52,401,046 bp number of sequenced bases = 52,378,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,579 duplication rate = 8.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7106 >>>>>>> ACTG content number of A's = 14,585,908 bp (27.85%) number of C's = 10,251,056 bp (19.57%) number of T's = 15,902,011 bp (30.36%) number of G's = 11,627,128 bp (22.2%) number of N's = 12,246 bp (0.02%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 462,869 number of insertions = 4,465 mapped reads with insertion percentage = 0.54% number of deletions = 13,848 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.2718X There is a 1.04% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.07% 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% 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 4143871 0.016625318658684506 0.3508926948603785 chr2 243199373 4596238 0.018899053658333238 0.3712812409476153 chr3 198022430 3447063 0.017407437127198166 0.213353651464722 chr4 191154276 3573735 0.01869555353289612 0.2347006904154196 chr5 180915260 2904007 0.016051752627169204 0.20831040233517556 chr6 171115067 3114444 0.018200875320932435 0.2638931346449981 chr7 159138663 2771192 0.017413694119071493 0.24089034422809272 chr8 146364022 2541345 0.01736318095986731 0.24752696370930016 chr9 141213431 2418255 0.017124822921411775 0.2280781601042193 chr10 135534747 2422052 0.01787033992102409 0.23366717015061175 chr11 135006516 2306654 0.0170855012657315 0.21877693633321835 chr12 133851895 2627069 0.01962668515077803 0.2288799384170281 chr13 115169878 1653349 0.01435574152470666 0.2296297250206184 chr14 107349540 1573853 0.014661012986175814 0.37575304983949726 chr15 102531392 1567400 0.015287025460456053 0.4746914407663291 chr16 90354753 1392952 0.01541647731580872 0.19633210097063353 chr17 81195210 1300678 0.01601914694228884 0.20449961364421382 chr18 78077248 1501376 0.01922936628094269 0.28650737596196457 chr19 59128983 1032524 0.017462231677483783 0.2681349734088747 chr20 63025520 1140366 0.018093718227156236 0.21123784978735252 chr21 48129895 692797 0.014394317710437556 0.18745061590435166 chr22 51304566 658740 0.01283979285586394 0.1791026025781298 chrMT 16571 10282 0.620481564178384 1.3508392480738096 chrX 155270560 2846362 0.018331627064396495 0.25491704743733434 chrY 59373566 164442 0.0027696163642924867 0.09884353563169702