BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124802.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 = 703,389 number of mapped reads = 702,727 (99.91%) number of supplementary alignments = 319,620 (45.44%) number of secondary alignments = 0 number of mapped bases = 105,753,664 bp number of sequenced bases = 105,707,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,020,869 duplication rate = 44.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 24.5762 >>>>>>> ACTG content number of A's = 30,608,485 bp (28.96%) number of C's = 20,865,650 bp (19.74%) number of T's = 33,321,929 bp (31.52%) number of G's = 20,911,336 bp (19.78%) number of N's = 1 bp (0%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 787,654 number of insertions = 13,023 mapped reads with insertion percentage = 1.84% number of deletions = 42,887 mapped reads with deletion percentage = 5.89% homopolymer indels = 80.38% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 57.0228X There is a 0% 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 61824 2.480395023770071E-4 0.2091246169571183 chr2 243199373 11814 4.857742787026018E-5 0.03828532646587564 chr3 198022430 10245 5.173656337819913E-5 0.047198511717833444 chr4 191154276 2924 1.529654507964028E-5 0.006448564089838812 chr5 180915260 3044 1.6825556893321214E-5 0.007119828556713775 chr6 171115067 5207 3.042981597874137E-5 0.02382483925727701 chr7 159138663 14772 9.282470847452074E-5 0.09097708397857185 chr8 146364022 77367264 0.528594820932155 237.50124464545212 chr9 141213431 3112 2.2037563834845142E-5 0.0048814642680721386 chr10 135534747 28233800 0.2083141085584496 115.56043002900738 chr11 135006516 2239 1.6584384712216408E-5 0.004250355295798861 chr12 133851895 3067 2.2913384976731184E-5 0.013118978994846412 chr13 115169878 3574 3.1032419779067576E-5 0.028515404910307785 chr14 107349540 11893 1.1078761958365169E-4 0.15424357929612376 chr15 102531392 1650 1.6092632391063216E-5 0.0045083504070361005 chr16 90354753 1440 1.5937180415954434E-5 0.0049119106626863045 chr17 81195210 1698 2.091256368448336E-5 0.006508016475046699 chr18 78077248 1081 1.3845262578926962E-5 0.0038194143069789333 chr19 59128983 1880 3.179489828194745E-5 0.00834323208990278 chr20 63025520 721 1.1439810413305594E-5 0.0033822595323309093 chr21 48129895 1670 3.4697769442463984E-5 0.01350097630434734 chr22 51304566 181 3.5279510989333776E-6 0.0018782807704106489 chrMT 16571 113 0.00681914187435882 0.08229605809791977 chrX 155270560 7351 4.734316666340355E-5 0.02243922550502346 chrY 59373566 1100 1.8526763240058714E-5 0.0043042328002911925