BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716148.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 = 2,074,552 number of mapped reads = 1,910,639 (92.1%) number of supplementary alignments = 11,993 (0.58%) number of secondary alignments = 0 number of mapped bases = 111,639,094 bp number of sequenced bases = 111,608,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,901 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3317 >>>>>>> ACTG content number of A's = 28,648,106 bp (25.67%) number of C's = 22,718,328 bp (20.36%) number of T's = 34,002,119 bp (30.47%) number of G's = 26,238,636 bp (23.51%) number of N's = 1,420 bp (0%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 550,541 number of insertions = 6,081 mapped reads with insertion percentage = 0.32% number of deletions = 19,275 mapped reads with deletion percentage = 1% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 0.334X There is a 3.14% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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% 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 9126317 0.036615022114628956 0.4534678068964541 chr2 243199373 11362633 0.046721473249850855 0.4102763305512542 chr3 198022430 8240369 0.04161331117894069 0.2472500748913704 chr4 191154276 6143518 0.032139056099378074 0.22445315152699769 chr5 180915260 5663091 0.03130245066115484 0.1982579347876823 chr6 171115067 6275803 0.036675922874751875 0.23088246194822398 chr7 159138663 6931979 0.04355936432619143 0.7449287778596224 chr8 146364022 7829923 0.053496227372051855 0.352504770896249 chr9 141213431 4692692 0.033231201641152674 0.23345629539071597 chr10 135534747 5441152 0.04014580851359098 0.4493929257168245 chr11 135006516 3384871 0.025071908381073992 0.22682798836961415 chr12 133851895 5354247 0.04000127902559766 0.2524628448511938 chr13 115169878 2882786 0.02503072895501374 0.17562427075601025 chr14 107349540 2842614 0.026479983053490495 0.18788824954506153 chr15 102531392 2714481 0.026474633251833742 0.18444078557779908 chr16 90354753 3480801 0.038523717728496255 0.23010439344113495 chr17 81195210 4800460 0.059122453159490565 0.2861308640888427 chr18 78077248 2514641 0.03220709059827519 0.36221767458927134 chr19 59128983 2286832 0.03867531427016088 0.41265357348269743 chr20 63025520 2561645 0.04064456747044689 0.23785497453465418 chr21 48129895 1141018 0.023707053589042737 0.18379333946105006 chr22 51304566 1710050 0.0333313413079062 0.20411282103491585 chrMT 16571 90389 5.4546496892161 3.771486727775228 chrX 155270560 3914793 0.025212719011253645 0.2038472856333056 chrY 59373566 251989 0.004244127765544687 0.11649464486768417