BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716648.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 = 2,392,354 number of mapped reads = 2,101,337 (87.84%) number of supplementary alignments = 58,364 (2.44%) number of secondary alignments = 0 number of mapped bases = 158,880,216 bp number of sequenced bases = 158,820,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,784 duplication rate = 2.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4307 >>>>>>> ACTG content number of A's = 41,659,955 bp (26.23%) number of C's = 32,666,956 bp (20.57%) number of T's = 47,708,915 bp (30.04%) number of G's = 36,765,590 bp (23.15%) number of N's = 19,523 bp (0.01%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,220,930 number of insertions = 12,574 mapped reads with insertion percentage = 0.59% number of deletions = 34,974 mapped reads with deletion percentage = 1.64% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.4277X There is a 4.4% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13740582 0.0551275737844601 0.6449488356919355 chr2 243199373 14031358 0.05769487736302675 0.634791487437579 chr3 198022430 11449168 0.057817531074636344 0.28217147260638353 chr4 191154276 6666464 0.03487478354917888 0.2237986657773838 chr5 180915260 10079297 0.055712807200453955 0.2726173732752365 chr6 171115067 11507757 0.06725157054697001 0.34363000769896507 chr7 159138663 8044193 0.05054832589614002 0.6056180034951213 chr8 146364022 11995151 0.08195423189450206 0.5557158491369114 chr9 141213431 7016080 0.04968422585809136 0.3922022464846652 chr10 135534747 7775671 0.0573703140494297 0.42246497328750976 chr11 135006516 6298971 0.04665679247659424 0.3459890531646672 chr12 133851895 5968601 0.04459108330143552 0.23995856892314957 chr13 115169878 4790741 0.04159717005170397 0.2267648077012118 chr14 107349540 3782446 0.0352348598792319 0.2398038671578561 chr15 102531392 3325924 0.03243810441976639 0.20121663840588214 chr16 90354753 3937575 0.0435790577613554 0.2775315765642834 chr17 81195210 4611927 0.0568004812106527 0.31010484642098646 chr18 78077248 4823076 0.06177313011852057 0.8368833892241705 chr19 59128983 2692705 0.04553951147781453 0.5334461582796731 chr20 63025520 3015550 0.04784649138951967 0.3024173804633886 chr21 48129895 3606370 0.07492993699653822 0.32610334158125304 chr22 51304566 2632325 0.051307811472374606 0.25924446101810505 chrMT 16571 11173 0.6742501961257619 1.2467954834907526 chrX 155270560 6716712 0.043258116670668284 0.2953098323609428 chrY 59373566 360399 0.006070024495412656 0.15620551738239452