BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708515.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 = 2,972,600 number of mapped reads = 2,071,833 (69.7%) number of supplementary alignments = 426 (0.01%) number of secondary alignments = 0 number of mapped bases = 99,472,904 bp number of sequenced bases = 99,454,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,489 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2565 >>>>>>> ACTG content number of A's = 28,763,564 bp (28.92%) number of C's = 18,468,341 bp (18.57%) number of T's = 31,845,296 bp (32.02%) number of G's = 20,376,234 bp (20.49%) number of N's = 1,314 bp (0%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 472,022 number of insertions = 4,606 mapped reads with insertion percentage = 0.22% number of deletions = 11,831 mapped reads with deletion percentage = 0.57% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.3127X There is a 2.77% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 8410225 0.033742042311702004 0.5355695491247382 chr2 243199373 8853344 0.03640364648473004 0.2763235856153296 chr3 198022430 7022090 0.03546108387822531 0.2143015226780923 chr4 191154276 6584736 0.034447233605174495 0.21432904386824786 chr5 180915260 6121081 0.033833967350239004 0.20894018022260402 chr6 171115067 6133872 0.0358464751674965 0.260120455722554 chr7 159138663 5532524 0.034765429693222945 0.36787464676249254 chr8 146364022 5058910 0.03456389029812258 0.6891751034861497 chr9 141213431 4204094 0.029771204978370647 0.22485076258915118 chr10 135534747 4695177 0.03464186936505662 0.2522027419965037 chr11 135006516 4577540 0.03390606717086159 0.2808671524269438 chr12 133851895 4711584 0.03519997979856766 0.21509519576410835 chr13 115169878 3293277 0.028594950842962603 0.1924875182141491 chr14 107349540 3210204 0.02990421756814235 0.19875237589585568 chr15 102531392 3013427 0.029390286635336035 0.19564831517427364 chr16 90354753 2694182 0.029817822644039545 0.2000833189662308 chr17 81195210 2801015 0.034497293621138486 0.2414251640082724 chr18 78077248 2644017 0.033864116214751834 0.3371000874423781 chr19 59128983 1798544 0.03041729975298239 0.37901689235189434 chr20 63025520 1960729 0.03111008048803088 0.2018800524135627 chr21 48129895 1322058 0.02746854112189524 0.2063153144521558 chr22 51304566 1138894 0.022198686955075306 0.18151187333984092 chrMT 16571 124019 7.484098726691207 5.651893839863438 chrX 155270560 2989340 0.019252458418389164 0.17503526096430969 chrY 59373566 578021 0.009735325649801799 0.11762244254333355