BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549089.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,073,567 number of mapped reads = 7,116,068 (88.14%) number of secondary alignments = 0 number of mapped bases = 282,692,073 bp number of sequenced bases = 282,664,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,467 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3287 >>>>>>> ACTG content number of A's = 83,788,071 bp (29.64%) number of C's = 57,852,152 bp (20.47%) number of T's = 84,766,711 bp (29.99%) number of G's = 56,189,677 bp (19.88%) number of N's = 68,368 bp (0.02%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,113,564 number of insertions = 6,425 mapped reads with insertion percentage = 0.09% number of deletions = 21,385 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 0.6565X There is a 7.77% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.15% 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 0.01% 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 22897141 0.09186392759278221 1.563809198569648 chr2 243199373 24765262 0.10183110957280306 0.5120006424141701 chr3 198022430 20017717 0.10108812925889255 0.3625768695523499 chr4 191154276 19550828 0.10227774344948475 0.37015501787827915 chr5 180915260 18252146 0.1008878189711581 0.3720260510527103 chr6 171115067 17352491 0.10140831724654616 0.47428169029450606 chr7 159138663 16013529 0.1006262632733065 0.756204437769498 chr8 146364022 15156520 0.10355359051283791 0.6785264788219039 chr9 141213431 11968227 0.0847527527321392 0.4876215308497601 chr10 135534747 13423215 0.09903892025563009 0.5385056431036251 chr11 135006516 13168592 0.09754041797508499 0.5151599630025195 chr12 133851895 12995309 0.097087224652292 0.3715033077167879 chr13 115169878 9771036 0.08484020448471778 0.3236306221598461 chr14 107349540 8805379 0.08202530723466538 0.36894871496373594 chr15 102531392 8106612 0.07906468294120107 0.3136497886712125 chr16 90354753 7489983 0.08289528498849419 0.37498232004043486 chr17 81195210 6830209 0.08412083668482415 0.3730309575846845 chr18 78077248 7860496 0.10067588447789554 0.9611216977462239 chr19 59128983 4665760 0.0789081726638187 1.182176092618153 chr20 63025520 5670919 0.08997813901416442 0.3497712418813661 chr21 48129895 3672356 0.07630093520877201 0.35786843820233327 chr22 51304566 2831156 0.05518331448315926 0.29533872238927467 chrMT 16571 18359 1.107899342224368 1.5881609652776392 chrX 155270560 9207487 0.05929963155926017 0.3493488712623177 chrY 59373566 2201344 0.037076162816294375 0.32457692622795165