BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080555.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,691,393 number of mapped reads = 2,222,594 (82.58%) number of supplementary alignments = 15,065 (0.56%) number of secondary alignments = 0 number of mapped bases = 147,355,561 bp number of sequenced bases = 147,299,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,700 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6347 >>>>>>> ACTG content number of A's = 40,272,500 bp (27.34%) number of C's = 26,066,765 bp (17.7%) number of T's = 48,177,921 bp (32.71%) number of G's = 32,662,678 bp (22.17%) number of N's = 119,482 bp (0.08%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,292,898 number of insertions = 12,011 mapped reads with insertion percentage = 0.54% number of deletions = 34,496 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.319X There is a 3.92% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.12% 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% 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 11704256 0.04695778069896965 0.38331206392882267 chr2 243199373 12289241 0.05053154886217573 0.32768494109871377 chr3 198022430 10006712 0.050533224948305096 0.2640825393016312 chr4 191154276 9959813 0.0521035323321776 0.27422644482642416 chr5 180915260 9238342 0.05106447073618887 0.26559911562500227 chr6 171115067 9219669 0.053879936826369594 0.3121744316969068 chr7 159138663 8410451 0.05284982820296787 0.5187818513746312 chr8 146364022 7986046 0.05456290344357987 0.45321940662977767 chr9 141213431 6502475 0.04604714264041924 0.3083182669324919 chr10 135534747 6401828 0.04723385066709129 0.29166223363931776 chr11 135006516 6987328 0.05175548712034018 0.29230316018320407 chr12 133851895 6273126 0.046866172496101005 0.25788046546189186 chr13 115169878 4819135 0.04184371021040762 0.241392753949929 chr14 107349540 4500777 0.04192637434682999 0.24998646269087516 chr15 102531392 4019119 0.039198911880568246 0.2327195781292129 chr16 90354753 3943784 0.043647775784412805 0.26068486833506893 chr17 81195210 3601117 0.04435134781965586 0.26098509898151945 chr18 78077248 3943325 0.050505430211884514 0.4653456920431284 chr19 59128983 2406939 0.04070658546587889 0.3124771416163948 chr20 63025520 2910614 0.04618151504343003 0.2557632682528236 chr21 48129895 1891883 0.03930785637492041 0.24126126305193912 chr22 51304566 1470565 0.02866343319228156 0.19713503740014357 chrMT 16571 37135 2.2409631283567677 3.5940387828822553 chrX 155270560 8515121 0.05484053770399231 0.2886576884843969 chrY 59373566 316760 0.005335034112655453 0.11096697936640454