BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081692.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 = 1,596,581 number of mapped reads = 1,344,088 (84.19%) number of supplementary alignments = 11,707 (0.73%) number of secondary alignments = 0 number of mapped bases = 89,986,631 bp number of sequenced bases = 89,954,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,965 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3648 >>>>>>> ACTG content number of A's = 25,151,309 bp (27.96%) number of C's = 15,849,275 bp (17.62%) number of T's = 29,419,734 bp (32.71%) number of G's = 19,472,248 bp (21.65%) number of N's = 61,462 bp (0.07%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 794,322 number of insertions = 7,620 mapped reads with insertion percentage = 0.56% number of deletions = 20,459 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.47% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 0.2656X There is a 2.4% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 7023596 0.028178850555401425 0.37021428790059707 chr2 243199373 7960772 0.032733521891111124 0.29353673944946046 chr3 198022430 6433884 0.032490682999900565 0.21021466216599688 chr4 191154276 6087154 0.0318441947905994 0.21592686343308076 chr5 180915260 5782609 0.03196308039465549 0.21030701001819127 chr6 171115067 5393648 0.03152059076130333 0.2285661077972721 chr7 159138663 4942999 0.03106095594129756 0.3004658663135546 chr8 146364022 4674786 0.03193944752351777 0.4784548846131925 chr9 141213431 3828671 0.02711265474457596 0.2578856601907534 chr10 135534747 3792145 0.02797913512171163 0.24567814944606237 chr11 135006516 3999170 0.029622051723784945 0.23534422685287948 chr12 133851895 4000087 0.029884425618329873 0.20473307644032995 chr13 115169878 3055252 0.026528221207284774 0.19109697312718138 chr14 107349540 2812416 0.02619867770276426 0.19652013593037085 chr15 102531392 2356951 0.02298760364045384 0.1778548929453643 chr16 90354753 2302844 0.02548669465124873 0.19513203513515115 chr17 81195210 2151561 0.026498619807744817 0.20279758923247235 chr18 78077248 2531323 0.032420750792855814 0.39732873084403153 chr19 59128983 1292260 0.021854933645653944 0.28308386980279565 chr20 63025520 1792473 0.028440431748916948 0.20225349607567103 chr21 48129895 1180514 0.024527666224910732 0.19223126465140358 chr22 51304566 885571 0.017261056257643813 0.15261561789114209 chrMT 16571 10000 0.6034638826866212 0.8881494449437247 chrX 155270560 5479839 0.03529219576460599 0.23373899400193288 chrY 59373566 216106 0.0036397679061419353 0.09637937931635791