BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008668.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 = 2,305,941 number of mapped reads = 2,117,133 (91.81%) number of supplementary alignments = 14,391 (0.62%) number of secondary alignments = 0 number of mapped bases = 141,007,337 bp number of sequenced bases = 140,931,676 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,244 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5417 >>>>>>> ACTG content number of A's = 38,981,618 bp (27.66%) number of C's = 26,144,149 bp (18.55%) number of T's = 43,693,498 bp (31%) number of G's = 32,067,525 bp (22.75%) number of N's = 44,886 bp (0.03%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,236,872 number of insertions = 11,804 mapped reads with insertion percentage = 0.55% number of deletions = 46,083 mapped reads with deletion percentage = 2.15% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 0.0455X std coverageData = 0.4634X There is a 3.97% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 12556086 0.050375344902350315 0.9323981398700276 chr2 243199373 12905486 0.05306545753306691 0.5839201353915773 chr3 198022430 10952871 0.055311264486553366 0.2621764472794293 chr4 191154276 6641878 0.03474616492492169 0.22748125321025003 chr5 180915260 7042149 0.03892512439249182 0.22090187792329882 chr6 171115067 7638915 0.04464197766991495 0.2846641456100071 chr7 159138663 6820445 0.04285850384453714 0.4884879607887497 chr8 146364022 12671595 0.08657588679819143 0.6028558028904039 chr9 141213431 4169801 0.02952835980594509 0.43143356528777776 chr10 135534747 8377557 0.061811138364393 0.4421359214672249 chr11 135006516 5943180 0.04402143078782953 0.5395712721897246 chr12 133851895 6173099 0.046118876389460155 0.2422678130844753 chr13 115169878 3510857 0.03048416010304361 0.18982616332339594 chr14 107349540 4489661 0.04182282476478241 0.2434195622061047 chr15 102531392 3533515 0.03446276238988348 0.2203801856608709 chr16 90354753 3704207 0.04099626059516758 0.27504604273230804 chr17 81195210 3834895 0.047230557073502245 0.35129658287439747 chr18 78077248 2185285 0.027988755443839414 0.7745350340427088 chr19 59128983 2886027 0.04880900792763508 0.6228895157484771 chr20 63025520 3313774 0.052578288921693944 0.26503847669532005 chr21 48129895 1410783 0.029311989980447702 0.20741511910648872 chr22 51304566 1679048 0.03272706760641928 0.19713660493425222 chrMT 16571 35221 2.1254601412105485 2.202899371137651 chrX 155270560 8128912 0.052353208489748476 0.30869819418498134 chrY 59373566 402090 0.006772205664722917 0.17596189661592235