BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124800.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 598,057 number of mapped reads = 597,214 (99.86%) number of supplementary alignments = 285,541 (47.74%) number of secondary alignments = 0 number of mapped bases = 90,739,950 bp number of sequenced bases = 90,682,694 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 880,494 duplication rate = 14.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9446 >>>>>>> ACTG content number of A's = 26,133,536 bp (28.82%) number of C's = 13,367,912 bp (14.74%) number of T's = 30,473,704 bp (33.6%) number of G's = 20,707,542 bp (22.84%) number of N's = 0 bp (0%) GC percentage = 37.58% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 778,129 number of insertions = 22,290 mapped reads with insertion percentage = 3.7% number of deletions = 52,480 mapped reads with deletion percentage = 8.52% homopolymer indels = 86.53% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 92.338X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 314352 0.00126118843250545 1.1041641068815895 chr2 243199373 39200 1.611846260804299E-4 0.04960739171050083 chr3 198022430 20906 1.0557389887600107E-4 0.023935302551729366 chr4 191154276 13023 6.812821702194095E-5 0.009188283645669695 chr5 180915260 11425 6.315111284697598E-5 0.007942342460826457 chr6 171115067 15445 9.026090028647214E-5 0.020120256314458032 chr7 159138663 13303 8.359376501736727E-5 0.009137768776605834 chr8 146364022 90169374 0.6160624227721755 424.6581047541985 chr9 141213431 11332 8.024732434976386E-5 0.009196454361812066 chr10 135534747 36962 2.727123547144704E-4 0.12138943204664748 chr11 135006516 9406 6.967071130107528E-5 0.008840075835345516 chr12 133851895 11864 8.863527856665757E-5 0.009410245807560998 chr13 115169878 5263 4.569771273005951E-5 0.006759211671251154 chr14 107349540 5784 5.388006320287912E-5 0.0073388371982262505 chr15 102531392 9589 9.352257696842738E-5 0.018836126509015887 chr16 90354753 9584 1.0607078965729672E-4 0.010366005277348388 chr17 81195210 6568 8.089147130723598E-5 0.009003869935563137 chr18 78077248 3487 4.466089788410575E-5 0.006682731723502444 chr19 59128983 6050 1.0231868862009685E-4 0.010696605444158845 chr20 63025520 7173 1.1381104035317757E-4 0.011851327196752207 chr21 48129895 2786 5.7885021357308173E-5 0.0077083835291812865 chr22 51304566 2616 5.098961367298185E-5 0.007135058227724996 chrMT 16571 459 0.027698992215315913 0.16410898222087597 chrX 155270560 10179 6.555653563689086E-5 0.00809285377595321 chrY 59373566 3820 6.433839597911299E-5 0.00804393157352332