BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548978.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 = 6,698,079 number of mapped reads = 2,913,887 (43.5%) number of secondary alignments = 0 number of mapped bases = 114,572,152 bp number of sequenced bases = 114,555,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,708 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6023 >>>>>>> ACTG content number of A's = 35,252,699 bp (30.77%) number of C's = 21,972,959 bp (19.18%) number of T's = 35,298,347 bp (30.81%) number of G's = 22,025,683 bp (19.23%) number of N's = 5,533 bp (0%) GC percentage = 38.41% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 404,828 number of insertions = 6,475 mapped reads with insertion percentage = 0.22% number of deletions = 13,616 mapped reads with deletion percentage = 0.47% homopolymer indels = 41.65% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.2999X There is a 3.14% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% 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% 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 9115730 0.03657254679417629 0.47363169035455227 chr2 243199373 10019113 0.041197116902106486 0.2829548971674501 chr3 198022430 8176105 0.04128878228592589 0.2344346334609861 chr4 191154276 8041892 0.04207016535690784 0.2414329179191403 chr5 180915260 7456429 0.041215036255095344 0.2355096961583327 chr6 171115067 6970395 0.040735132926663906 0.2508608508496727 chr7 159138663 6505955 0.04088230275002373 0.4063551858178527 chr8 146364022 5962101 0.040734744225599376 0.487823369524513 chr9 141213431 4850761 0.034350564005487555 0.2511440054060618 chr10 135534747 5382533 0.03971330687620644 0.2640571356520607 chr11 135006516 5284512 0.039142644048380595 0.27518010020454303 chr12 133851895 5160633 0.03855479969110635 0.23095327512397976 chr13 115169878 3972247 0.034490329146654126 0.21327996926317225 chr14 107349540 3580282 0.033351628707491435 0.23567904782469748 chr15 102531392 3251428 0.03171153669697569 0.20372197286952914 chr16 90354753 2979288 0.03297322942158892 0.21390024439075495 chr17 81195210 2809636 0.03460346983522797 0.22001307226393402 chr18 78077248 3131420 0.04010669023580339 0.3998480222538744 chr19 59128983 1950110 0.03298061121734497 0.4247137525600353 chr20 63025520 2302210 0.03652821904523755 0.2241513443374676 chr21 48129895 1534058 0.031873287901417614 0.21986459034297792 chr22 51304566 1166611 0.022738931267832965 0.20402990023708623 chrMT 16571 2675 0.16142658861867118 0.40746044022222555 chrX 155270560 3955013 0.025471750729822832 0.20527893122211238 chrY 59373566 1011015 0.01702803230649815 0.20345699982796506