BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084840.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,872,231 number of mapped reads = 2,557,252 (89.03%) number of supplementary alignments = 23,073 (0.8%) number of secondary alignments = 0 number of mapped bases = 175,386,386 bp number of sequenced bases = 175,320,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,862 duplication rate = 4.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9199 >>>>>>> ACTG content number of A's = 50,501,805 bp (28.81%) number of C's = 31,996,210 bp (18.25%) number of T's = 56,272,312 bp (32.1%) number of G's = 36,522,442 bp (20.83%) number of N's = 27,310 bp (0.02%) GC percentage = 39.08% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,443,520 number of insertions = 14,602 mapped reads with insertion percentage = 0.57% number of deletions = 37,443 mapped reads with deletion percentage = 1.45% homopolymer indels = 48.69% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.461X There is a 4.52% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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 14778334 0.05929106190672239 0.8760882419807499 chr2 243199373 12259226 0.05040813160320113 0.4300268893945331 chr3 198022430 10561930 0.05333703863749172 0.2762532898735151 chr4 191154276 12865786 0.06730577138645855 0.3353737920373228 chr5 180915260 11469512 0.06339715068811774 0.30264095702973703 chr6 171115067 11095750 0.0648437930950873 0.3110909344133174 chr7 159138663 10135334 0.06368869644204564 0.45163589568626555 chr8 146364022 9259283 0.06326201530591992 0.8776044689439687 chr9 141213431 7199277 0.05098153163632148 0.4015479185505595 chr10 135534747 7371218 0.05438618629656644 0.4087747597394569 chr11 135006516 8498746 0.06295063565672637 0.373479563171908 chr12 133851895 8093511 0.060466166728532306 0.29617559812389554 chr13 115169878 6105820 0.053015772058037605 0.27613963951935644 chr14 107349540 5502316 0.051256074315735305 0.27927263167800875 chr15 102531392 5362006 0.052296237234348675 0.27303929566828383 chr16 90354753 4698181 0.05199705432208973 0.2931150578349988 chr17 81195210 4368705 0.05380495967680852 0.3150307262429946 chr18 78077248 5159138 0.06607735457069389 0.7199253048555958 chr19 59128983 3036659 0.05135652341593631 0.5753377761083165 chr20 63025520 3536051 0.05610506664601895 0.2915883294855941 chr21 48129895 2357540 0.04898286189903386 0.2924389401001942 chr22 51304566 1780199 0.03469864651033204 0.2193515087937301 chrMT 16571 68965 4.161788666948283 2.769936581478816 chrX 155270560 9387968 0.06046199614402112 0.31581603178227136 chrY 59373566 434931 0.007325330602510888 0.179854667161904