BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524459.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 = 4,517,531 number of mapped reads = 4,169,931 (92.31%) number of supplementary alignments = 9,063 (0.2%) number of secondary alignments = 0 number of mapped bases = 242,654,586 bp number of sequenced bases = 242,579,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,556 duplication rate = 6.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4893 >>>>>>> ACTG content number of A's = 57,789,552 bp (23.82%) number of C's = 45,028,532 bp (18.56%) number of T's = 78,073,410 bp (32.18%) number of G's = 61,683,642 bp (25.43%) number of N's = 4,547 bp (0%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,131,692 number of insertions = 14,845 mapped reads with insertion percentage = 0.35% number of deletions = 43,226 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.0784X std coverageData = 0.6372X There is a 5.91% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 23799926 0.0954859245867235 1.2817934921519833 chr2 243199373 19308441 0.0793934653770674 0.7315579669965282 chr3 198022430 13304803 0.06718836345963435 0.3360337436647788 chr4 191154276 13705492 0.0716985896773766 0.43358831972506584 chr5 180915260 13363160 0.07386419476168014 0.3512743768023963 chr6 171115067 10444184 0.0610360278794152 0.473790687151125 chr7 159138663 12037950 0.07564440829818961 0.8335687196428433 chr8 146364022 22372721 0.15285669725583245 0.6449255298303199 chr9 141213431 10281692 0.07280958990366858 0.5375352371093698 chr10 135534747 12663509 0.09343367129316292 0.6268361421365152 chr11 135006516 8334212 0.06173192410950002 0.6240760284969177 chr12 133851895 11231668 0.08391116166117783 0.3758049775868594 chr13 115169878 5416987 0.04703475504245997 0.2856140283000883 chr14 107349540 5767207 0.05372363030153646 0.3104142425017445 chr15 102531392 6461090 0.06301572497913614 0.3430497030204686 chr16 90354753 7563279 0.08370648747166627 0.4171879102159817 chr17 81195210 8413539 0.10362112494074466 0.45424277690012205 chr18 78077248 5705496 0.0730750141193501 1.0394336960457746 chr19 59128983 4891904 0.08273276068353823 0.8546986240601182 chr20 63025520 6946580 0.11021852735209484 0.43953885767040535 chr21 48129895 3333533 0.06926117333104508 0.3859997366266936 chr22 51304566 1969229 0.03838311389282584 0.25035772430812836 chrMT 16571 160216 9.66845694285197 7.15216724998873 chrX 155270560 14426253 0.09291042036558637 0.48823580117601023 chrY 59373566 751515 0.012657400433047932 0.30710684852257747