BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006435.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 = 1,109,374 number of mapped reads = 1,053,368 (94.95%) number of supplementary alignments = 3,059 (0.28%) number of secondary alignments = 0 number of mapped bases = 59,361,067 bp number of sequenced bases = 59,342,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,554 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9021 >>>>>>> ACTG content number of A's = 16,645,167 bp (28.05%) number of C's = 12,697,621 bp (21.4%) number of T's = 16,340,222 bp (27.54%) number of G's = 13,623,342 bp (22.96%) number of N's = 36,132 bp (0.06%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 306,120 number of insertions = 3,980 mapped reads with insertion percentage = 0.38% number of deletions = 10,622 mapped reads with deletion percentage = 1% homopolymer indels = 41.4% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 0.1854X There is a 1.76% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4881952 0.01958651890379844 0.19011268150550836 chr2 243199373 5010770 0.020603548184312138 0.17738651130484495 chr3 198022430 3866542 0.019525777963637754 0.1484965237263028 chr4 191154276 3599270 0.018829136733514662 0.15283142048140938 chr5 180915260 3557684 0.01966491936611649 0.1497020656596441 chr6 171115067 3675660 0.021480633262996065 0.15993888539659606 chr7 159138663 3303678 0.020759744600845363 0.17422576467735748 chr8 146364022 3073835 0.021001301808992377 0.4526389809957805 chr9 141213431 2479092 0.017555638882536605 0.1494641182776169 chr10 135534747 2891646 0.021335089812799076 0.179281628782287 chr11 135006516 2763323 0.020468071333682888 0.15874266006519397 chr12 133851895 2641120 0.019731659383679254 0.1512381537022591 chr13 115169878 1850392 0.016066631589207726 0.13582654514195172 chr14 107349540 1833168 0.017076626504407937 0.14141466696211352 chr15 102531392 1805066 0.0176050082300648 0.14179703119305992 chr16 90354753 1922442 0.021276600689727965 0.1811763223248887 chr17 81195210 1767466 0.021768106763933488 0.16265627558462742 chr18 78077248 1538819 0.019708929802443858 0.1814130909112446 chr19 59128983 1388699 0.02348592736661816 0.19149333794383636 chr20 63025520 1238762 0.019654927083505223 0.15238228437966547 chr21 48129895 1091287 0.02267378725841808 0.17105516475430285 chr22 51304566 893177 0.017409308169569156 0.15448728388944866 chrMT 16571 32239 1.945507211393398 1.8210537121093562 chrX 155270560 1745463 0.011241429154374146 0.11403293708991907 chrY 59373566 509515 0.008581512520235014 0.1428638811926783