BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236103.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 = 1,339,722 number of mapped reads = 799,916 (59.71%) number of supplementary alignments = 4,748 (0.35%) number of secondary alignments = 0 number of mapped bases = 52,098,181 bp number of sequenced bases = 52,071,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,234 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.925 >>>>>>> ACTG content number of A's = 14,403,836 bp (27.66%) number of C's = 9,058,860 bp (17.4%) number of T's = 17,097,090 bp (32.83%) number of G's = 11,485,137 bp (22.06%) number of N's = 26,287 bp (0.05%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 417,939 number of insertions = 3,560 mapped reads with insertion percentage = 0.44% number of deletions = 15,451 mapped reads with deletion percentage = 1.91% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.1701X There is a 1.47% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4255518 0.017073249338062833 0.17043821021007743 chr2 243199373 3293925 0.013544134425050511 0.1705440393551804 chr3 198022430 4283941 0.02163361493947933 0.16366226168000303 chr4 191154276 4076267 0.021324487661474024 0.16556405257035953 chr5 180915260 2351959 0.013000335074000944 0.12713407688633926 chr6 171115067 6482069 0.03788134565613675 0.2547121770292677 chr7 159138663 2644215 0.016615792480297514 0.25170973383246315 chr8 146364022 3431499 0.023444962451223156 0.2266947625063589 chr9 141213431 2197831 0.015563894910251137 0.16619576371056058 chr10 135534747 1174179 0.008663306096701535 0.12822485708233386 chr11 135006516 2721888 0.020161160221333317 0.16315911079865347 chr12 133851895 2284728 0.01706907474115327 0.14719768688961637 chr13 115169878 2528799 0.02195712146191559 0.1657344730209202 chr14 107349540 1915615 0.01784465028913957 0.15178298741784021 chr15 102531392 1699376 0.01657420197708815 0.14398711463216063 chr16 90354753 730304 0.00808262958784249 0.10578488221327324 chr17 81195210 1524961 0.018781415800267036 0.16430019529941217 chr18 78077248 872351 0.011172921975938496 0.22272945063699442 chr19 59128983 269025 0.0045497992076068685 0.11382003129964613 chr20 63025520 1121666 0.017797013019487978 0.1489408893054721 chr21 48129895 463847 0.009637398959627898 0.11473376108594588 chr22 51304566 149017 0.002904556292319089 0.058501433169527835 chrMT 16571 63986 3.8613239997586146 2.819453639687932 chrX 155270560 1457240 0.009385166125503766 0.11140021018815847 chrY 59373566 103975 0.0017512001889864591 0.05800822556379795