BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238629.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 = 1,473,964 number of mapped reads = 1,325,703 (89.94%) number of supplementary alignments = 10,074 (0.68%) number of secondary alignments = 0 number of mapped bases = 80,267,459 bp number of sequenced bases = 80,229,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,537 duplication rate = 17.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.6335 >>>>>>> ACTG content number of A's = 19,451,875 bp (24.25%) number of C's = 13,774,070 bp (17.17%) number of T's = 27,282,884 bp (34.01%) number of G's = 19,717,014 bp (24.58%) number of N's = 3,858 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 443,171 number of insertions = 4,742 mapped reads with insertion percentage = 0.35% number of deletions = 22,213 mapped reads with deletion percentage = 1.66% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.366X There is a 1.53% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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% 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 10867957 0.04360252727314168 0.4072303311227584 chr2 243199373 2138906 0.008794866424265 0.7448989134885773 chr3 198022430 7952051 0.040157324602066544 0.31857346478516124 chr4 191154276 8593730 0.04495703773846001 0.33474724963721453 chr5 180915260 2311967 0.012779281305512868 0.17965011868789768 chr6 171115067 1287692 0.0075252987511614045 0.2747428674349697 chr7 159138663 3506429 0.022033797028947012 0.284809129168686 chr8 146364022 3168491 0.021648018117457854 0.25882788323472555 chr9 141213431 3938886 0.027893139994594425 0.30488315396637117 chr10 135534747 3608492 0.02662410990445129 0.27374576256054106 chr11 135006516 2287156 0.016941078606902204 0.20732828403323922 chr12 133851895 1336443 0.009984490693986813 0.16962269662026408 chr13 115169878 409714 0.0035574753322218508 0.17354191134617958 chr14 107349540 2405965 0.022412438842308965 0.26673409099183776 chr15 102531392 590220 0.005756480902941413 0.18159168192143912 chr16 90354753 4456845 0.04932607142426697 0.3855112101226794 chr17 81195210 624588 0.0076924242205913375 0.12952945495825127 chr18 78077248 8452685 0.10826053961328146 0.8630822659445636 chr19 59128983 547086 0.009252416873126331 0.1959950203145468 chr20 63025520 1523070 0.02416592516809064 0.25043082268318495 chr21 48129895 648297 0.01346973642888687 0.19224553969245523 chr22 51304566 966738 0.018843118173926275 0.21703955398693742 chrMT 16571 41509 2.504918230643896 3.0038557174027427 chrX 155270560 8372079 0.05391929416626049 0.3769530566192577 chrY 59373566 230463 0.0038815758514487743 0.1383102114568463