BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080760.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 = 9,881,354 number of mapped reads = 6,626,429 (67.06%) number of supplementary alignments = 52,047 (0.53%) number of secondary alignments = 0 number of mapped bases = 421,950,930 bp number of sequenced bases = 421,802,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,025,053 duplication rate = 11.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4498 >>>>>>> ACTG content number of A's = 129,574,882 bp (30.72%) number of C's = 85,136,488 bp (20.18%) number of T's = 110,923,610 bp (26.3%) number of G's = 96,031,811 bp (22.77%) number of N's = 135,777 bp (0.03%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,637,563 number of insertions = 31,362 mapped reads with insertion percentage = 0.47% number of deletions = 79,996 mapped reads with deletion percentage = 1.19% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.1363X std coverageData = 0.8647X There is a 8.14% of reference with a coverageData >= 1X There is a 2.76% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 52127263 0.20913594032730615 1.2140225018318467 chr2 243199373 31916268 0.13123499294547936 0.7865453862076843 chr3 198022430 26161706 0.1321148619376098 0.5767655399755135 chr4 191154276 24454957 0.1279330889778265 0.7111179208980855 chr5 180915260 26790811 0.14808486028210113 0.6225424330074627 chr6 171115067 28689786 0.16766370433060696 1.2805946372031571 chr7 159138663 27353828 0.17188675262403078 1.1745702598275942 chr8 146364022 20647047 0.14106640906602033 1.2296255441612258 chr9 141213431 15165152 0.10739171120344777 0.6608443822707337 chr10 135534747 18215298 0.1343957797036357 0.9314088404839843 chr11 135006516 16818395 0.124574690898623 0.8230817600112226 chr12 133851895 16350592 0.12215435575267725 0.6039305447661941 chr13 115169878 15863340 0.13773861946784385 0.5979450509450621 chr14 107349540 12238903 0.11400983180738362 0.6387639487705878 chr15 102531392 10772288 0.10506331563312825 0.5210339597216497 chr16 90354753 11831596 0.13094602781991999 0.6464526104745822 chr17 81195210 10185783 0.12544807754053472 0.6065793576912191 chr18 78077248 6496755 0.08320932366878504 0.9960849615092432 chr19 59128983 9322114 0.15765726936314803 1.3750846426044918 chr20 63025520 7657487 0.1214981962862028 0.592699250734564 chr21 48129895 6370597 0.132362578393325 0.7143386595834286 chr22 51304566 3941119 0.07681809451423875 0.44247978735703947 chrMT 16571 332807 20.083700440528634 14.274946997156002 chrX 155270560 20900200 0.13460504038885415 0.6249513647172678 chrY 59373566 1346838 0.022684135226103817 0.6192876335567558