BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716453.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 = 464,103 number of mapped reads = 416,216 (89.68%) number of supplementary alignments = 6,433 (1.39%) number of secondary alignments = 0 number of mapped bases = 33,145,318 bp number of sequenced bases = 33,130,536 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,776 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2622 >>>>>>> ACTG content number of A's = 8,221,988 bp (24.82%) number of C's = 6,245,464 bp (18.85%) number of T's = 10,105,298 bp (30.5%) number of G's = 8,555,659 bp (25.82%) number of N's = 2,127 bp (0.01%) GC percentage = 44.68% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 274,326 number of insertions = 2,916 mapped reads with insertion percentage = 0.69% number of deletions = 8,519 mapped reads with deletion percentage = 2.01% homopolymer indels = 43.78% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1597X There is a 1% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% 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 2674455 0.010729983296611326 0.23768987447794845 chr2 243199373 2833932 0.011652710963198084 0.21311182682953878 chr3 198022430 2191297 0.011065902988868483 0.11020558684529834 chr4 191154276 2141981 0.011205509208698004 0.11494409433735049 chr5 180915260 1970136 0.010889827646379857 0.10987502584677568 chr6 171115067 1907828 0.011149386395062452 0.12227665298121326 chr7 159138663 1841633 0.011572505168024442 0.20343236771130424 chr8 146364022 1666764 0.011387798567054956 0.19390592840996898 chr9 141213431 1403652 0.009939932696628552 0.16155205366475897 chr10 135534747 1570104 0.011584512715399838 0.15552289478029338 chr11 135006516 1479894 0.010961648695534074 0.15599275244148264 chr12 133851895 1489573 0.011128516335162831 0.11225656064289578 chr13 115169878 1010472 0.00877375245634974 0.09691749010706775 chr14 107349540 1010513 0.009413296042069672 0.11784247337821636 chr15 102531392 947838 0.009244368788048836 0.10052183123637183 chr16 90354753 961907 0.01064589264053436 0.11656734105345781 chr17 81195210 917287 0.011297304360688272 0.11522488731284418 chr18 78077248 934763 0.011972284166573085 0.30766456615181365 chr19 59128983 739646 0.012509026241834736 0.19129010591407125 chr20 63025520 665992 0.010567021105101552 0.10961981537213926 chr21 48129895 426051 0.008852107406425882 0.10150180022676492 chr22 51304566 368874 0.007189886373856081 0.08804719536810832 chrMT 16571 3150 0.19009112304628567 0.47473066883502524 chrX 155270560 1896499 0.01221415701727359 0.13419112499773478 chrY 59373566 91077 0.0015339654687407524 0.05540920898473978