BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548969.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 = 11,161,850 number of mapped reads = 4,907,079 (43.96%) number of secondary alignments = 0 number of mapped bases = 193,715,019 bp number of sequenced bases = 193,688,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,267 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4104 >>>>>>> ACTG content number of A's = 59,838,883 bp (30.89%) number of C's = 36,763,712 bp (18.98%) number of T's = 60,009,981 bp (30.98%) number of G's = 37,066,481 bp (19.14%) number of N's = 9,841 bp (0.01%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 612,008 number of insertions = 8,446 mapped reads with insertion percentage = 0.17% number of deletions = 20,838 mapped reads with deletion percentage = 0.42% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.0626X std coverageData = 0.4251X There is a 5.01% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 15253398 0.06119703107981424 0.6753067125913891 chr2 243199373 16868421 0.06936046253704774 0.4097700222552595 chr3 198022430 13955314 0.07047340041226643 0.3224871712694433 chr4 191154276 14038588 0.07344114028607972 0.3346830912826464 chr5 180915260 12677704 0.07007537119864847 0.3241032305881245 chr6 171115067 11798199 0.06894891961793172 0.3699054024237006 chr7 159138663 11123982 0.06990119051081886 0.6151740220543273 chr8 146364022 10280140 0.07023679630777023 0.6581573012597468 chr9 141213431 8319246 0.05891256901760287 0.3656875005786889 chr10 135534747 9086852 0.06704444580547304 0.36345025797637637 chr11 135006516 8886861 0.06582542282625825 0.39654078469337734 chr12 133851895 8768086 0.06550587871766776 0.3189909046698561 chr13 115169878 6635015 0.05761068011203416 0.2895476403996859 chr14 107349540 6120058 0.05701056567172994 0.3348297724303782 chr15 102531392 5505977 0.053700402311908535 0.28004626470382343 chr16 90354753 4983338 0.05515302554144551 0.294687622624189 chr17 81195210 4435300 0.05462514352755538 0.29717944655857165 chr18 78077248 5489688 0.07031098227232599 0.5941126179442923 chr19 59128983 3176732 0.053725463196280576 0.622945788323991 chr20 63025520 3675593 0.05831912215876997 0.297893863513208 chr21 48129895 2586249 0.05373477336694792 0.3053239297538478 chr22 51304566 1828269 0.03563560015301562 0.2574930456653854 chrMT 16571 10225 0.6170418200470702 0.9095788800666746 chrX 155270560 6767241 0.0435835421730945 0.28458226643972573 chrY 59373566 1444543 0.024329732864621943 0.24856170058437277