BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004053.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 = 3,362,631 number of mapped reads = 3,080,236 (91.6%) number of supplementary alignments = 22,605 (0.67%) number of secondary alignments = 0 number of mapped bases = 206,925,754 bp number of sequenced bases = 206,838,260 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,288 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3026 >>>>>>> ACTG content number of A's = 56,506,179 bp (27.32%) number of C's = 38,879,849 bp (18.8%) number of T's = 64,653,553 bp (31.26%) number of G's = 46,570,773 bp (22.52%) number of N's = 227,906 bp (0.11%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,611,543 number of insertions = 13,939 mapped reads with insertion percentage = 0.45% number of deletions = 49,690 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.0668X std coverageData = 0.4806X There is a 4.88% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% 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% 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 25291850 0.10147156263253602 0.9319918654561278 chr2 243199373 10732742 0.04413145423693177 0.576161102371208 chr3 198022430 16541018 0.0835310323179046 0.3733041796817491 chr4 191154276 8871751 0.0464114702827783 0.2882491429505892 chr5 180915260 10242578 0.05661533471526946 0.31500974698488005 chr6 171115067 14778627 0.08636660265574393 0.4123207033272154 chr7 159138663 12761817 0.08019306408273645 0.5235290807258426 chr8 146364022 9898461 0.06762905845809566 0.6004026032982055 chr9 141213431 6030118 0.042702156284270154 0.3424617134131924 chr10 135534747 9899331 0.0730390635546765 0.40945600891376177 chr11 135006516 6590991 0.04881979918658148 0.32873233681126274 chr12 133851895 10818461 0.080824115340317 0.37073550086380763 chr13 115169878 6311354 0.05480038799728519 0.3070817288248125 chr14 107349540 4359384 0.0406092471379011 0.26866792818991175 chr15 102531392 6277112 0.061221367208200976 0.32570835419216454 chr16 90354753 6717266 0.07434325009996984 0.36620911659255867 chr17 81195210 7996999 0.09849101935939325 0.43145123453141676 chr18 78077248 5874561 0.07524036964007748 0.694788790518713 chr19 59128983 4748452 0.08030667464718613 0.616429657892908 chr20 63025520 5621327 0.08919128315006365 0.4044431780135802 chr21 48129895 4020867 0.08354198570348013 0.38091951484865555 chr22 51304566 3420761 0.0666755664593284 0.3342681065204474 chrMT 16571 13758 0.8302456098002534 1.1375037641568218 chrX 155270560 8724369 0.05618817243912819 0.3260434090764476 chrY 59373566 381799 0.006430454252991979 0.11629111276316959