BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230388.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 = 2,328,927 number of mapped reads = 1,583,916 (68.01%) number of supplementary alignments = 9,167 (0.39%) number of secondary alignments = 0 number of mapped bases = 100,584,199 bp number of sequenced bases = 100,539,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,621 duplication rate = 5.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9385 >>>>>>> ACTG content number of A's = 26,592,665 bp (26.45%) number of C's = 16,929,862 bp (16.84%) number of T's = 34,386,837 bp (34.2%) number of G's = 22,451,811 bp (22.33%) number of N's = 178,431 bp (0.18%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 1,125,401 number of insertions = 8,553 mapped reads with insertion percentage = 0.54% number of deletions = 27,992 mapped reads with deletion percentage = 1.75% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.3702X There is a 2.58% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 4066283 0.016314033576670606 0.6785131150791398 chr2 243199373 17760498 0.07302855176357712 0.48540872096652105 chr3 198022430 6954121 0.0351178449835203 0.22666533418149273 chr4 191154276 10844961 0.056734074837018034 0.29212044815454574 chr5 180915260 2908758 0.016078013540704084 0.15518802170859247 chr6 171115067 3193918 0.01866532302500282 0.2086855328808526 chr7 159138663 5225055 0.03283334735569571 0.7391358156201739 chr8 146364022 2460384 0.016810032727851656 0.30851621595010625 chr9 141213431 2061917 0.014601422721610666 0.2842834926427617 chr10 135534747 3891894 0.02871510137544286 0.25213663095339667 chr11 135006516 3210447 0.02377994111039796 0.29369585040114665 chr12 133851895 7921059 0.059177787509097274 0.2980890535099157 chr13 115169878 1203619 0.010450814231130817 0.12025615691486506 chr14 107349540 3718871 0.03464263563681782 0.2327926948666142 chr15 102531392 1245893 0.012151332150059955 0.13251422001707613 chr16 90354753 1149981 0.01272739907772201 0.14911940578024663 chr17 81195210 1010721 0.012448037267223029 0.14372773638290667 chr18 78077248 3843146 0.04922235476332362 0.5138681272890208 chr19 59128983 4496607 0.07604742669090046 0.4252322171163773 chr20 63025520 2880684 0.04570662804527436 0.2618142796531975 chr21 48129895 1438941 0.029897031772041057 0.21335275507105786 chr22 51304566 1376402 0.026828060488807176 0.19482844869728352 chrMT 16571 76767 4.632611188220385 3.9554229418912037 chrX 155270560 7409718 0.0477213323633276 0.30552210184170664 chrY 59373566 233554 0.00393363605615334 0.0836624160906465