BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708636.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,884,757 number of mapped reads = 4,629,665 (94.78%) number of supplementary alignments = 133 (0%) number of secondary alignments = 0 number of mapped bases = 230,903,827 bp number of sequenced bases = 230,881,137 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,777 duplication rate = 0.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7246 >>>>>>> ACTG content number of A's = 71,068,277 bp (30.78%) number of C's = 44,148,595 bp (19.12%) number of T's = 71,085,973 bp (30.79%) number of G's = 44,571,287 bp (19.3%) number of N's = 7,005 bp (0%) GC percentage = 38.43% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 376,598 number of insertions = 15,968 mapped reads with insertion percentage = 0.34% number of deletions = 13,375 mapped reads with deletion percentage = 0.29% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.0746X std coverageData = 0.296X There is a 6.66% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.01% 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 22057402 0.08849487279712735 0.32494316989417826 chr2 243199373 18279304 0.07516180561863538 0.29326653729705604 chr3 198022430 16305138 0.08233985412662596 0.30904881157564995 chr4 191154276 12481658 0.06529625316882788 0.2740304170660943 chr5 180915260 14160216 0.07826988171147088 0.30307567361510235 chr6 171115067 14325044 0.08371585419769026 0.30999697002056553 chr7 159138663 17277644 0.10856974461322451 0.3602377779726776 chr8 146364022 16326543 0.11154751541331653 0.36399532106466553 chr9 141213431 8735749 0.06186202642438452 0.265505650810262 chr10 135534747 10697901 0.07893105817359146 0.3019869766042037 chr11 135006516 11350074 0.08407056441631307 0.31856724115421453 chr12 133851895 11093326 0.08287761633856584 0.31062928070151125 chr13 115169878 10654786 0.09251365187692566 0.3326923311541858 chr14 107349540 5680775 0.05291848479276204 0.24897398111887362 chr15 102531392 7261779 0.07082493330432889 0.2888943533584124 chr16 90354753 4001457 0.04428607092755818 0.22363862143483898 chr17 81195210 4670813 0.05752572103699221 0.2561594821279178 chr18 78077248 7920883 0.10144931081587302 0.3438263167536372 chr19 59128983 2317270 0.03919008720308956 0.20978691363418214 chr20 63025520 3543164 0.056217925691053404 0.2529186797204206 chr21 48129895 2715464 0.05641948730617426 0.25737872280960505 chr22 51304566 2102930 0.04098913925127054 0.21817270857152365 chrMT 16571 840 0.05069096614567618 0.2303688258747793 chrX 155270560 6502314 0.041877314025273046 0.2189902635398984 chrY 59373566 441353 0.007433493214808759 0.09196366388551516