BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006409.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,467,772 number of mapped reads = 6,513,801 (87.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,289,991 number of mapped paired reads (second in pair) = 3,223,810 number of mapped paired reads (both in pair) = 5,906,364 number of mapped paired reads (singletons) = 607,437 number of mapped bases = 252,063,465 bp number of sequenced bases = 252,034,656 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 266,325 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 85,581.1867 std insert size = 2,781,376.3904 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 47.9086 >>>>>>> ACTG content number of A's = 70,173,123 bp (27.84%) number of C's = 54,371,070 bp (21.57%) number of T's = 71,468,158 bp (28.36%) number of G's = 56,011,575 bp (22.22%) number of N's = 10,730 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 866,368 number of insertions = 6,705 mapped reads with insertion percentage = 0.1% number of deletions = 21,807 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.73% >>>>>>> Coverage mean coverageData = 0.0814X std coverageData = 0.4697X There is a 6.84% of reference with a coverageData >= 1X There is a 0.98% 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 0.02% 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 0.01% 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 20934266 0.08398882183727839 0.7021913298829511 chr2 243199373 20484433 0.08422897126465864 0.42309241050602814 chr3 198022430 17146332 0.086587827449648 0.3333659413979425 chr4 191154276 15741430 0.08234934802086248 0.38708283365841406 chr5 180915260 14889727 0.08230221707113043 0.32609003704461553 chr6 171115067 14333965 0.08376798870668706 0.35875558973476135 chr7 159138663 13403896 0.08422777813585125 0.5236753123165856 chr8 146364022 12805644 0.08749174711801784 0.9595965047725983 chr9 141213431 10354963 0.07332845697942146 0.35524110766824785 chr10 135534747 11662192 0.0860457724542032 0.535432966521608 chr11 135006516 12023362 0.08905764222520934 0.405795669937537 chr12 133851895 11090002 0.08285278292100384 0.3293510538219917 chr13 115169878 7764053 0.06741392050445691 0.2947833513174157 chr14 107349540 7616146 0.07094716940566304 0.34274090300993637 chr15 102531392 7496339 0.07311262291260028 0.3069882914078297 chr16 90354753 8184354 0.09058022658752661 0.43772272561531506 chr17 81195210 7114622 0.08762366646998018 0.3544332791775422 chr18 78077248 6415665 0.08217073685793844 0.609560225479367 chr19 59128983 5178866 0.08758591366267876 0.5347084480880994 chr20 63025520 5660198 0.0898080333172975 0.3551762818541142 chr21 48129895 3225147 0.06700922576290681 0.34241741986594454 chr22 51304566 3373809 0.06576040424939955 0.29965562851538463 chrMT 16571 7822 0.4720294490374751 0.8210092701609611 chrX 155270560 14436808 0.09297839848069074 0.38005393654955805 chrY 59373566 719424 0.012116907379287275 0.3187058697869928