BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819009.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 672,238 number of mapped reads = 657,052 (97.74%) number of supplementary alignments = 10,189 (1.52%) number of secondary alignments = 0 number of mapped bases = 60,666,788 bp number of sequenced bases = 60,629,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 170,156 duplication rate = 22.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1471 >>>>>>> ACTG content number of A's = 17,626,351 bp (29.07%) number of C's = 12,940,284 bp (21.34%) number of T's = 17,180,418 bp (28.34%) number of G's = 12,879,096 bp (21.24%) number of N's = 2,989 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 414,589 number of insertions = 8,744 mapped reads with insertion percentage = 1.29% number of deletions = 20,208 mapped reads with deletion percentage = 3% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.3048X There is a 1.32% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 5958052 0.023903860203421518 0.6035630053956882 chr2 243199373 4757681 0.019562883494769538 0.3667542861453928 chr3 198022430 3073834 0.015522655691074996 0.17208723730186595 chr4 191154276 3339467 0.01747000940747985 0.21574587996828107 chr5 180915260 4492786 0.024833648637489176 0.2220084445368761 chr6 171115067 2513740 0.014690348687997182 0.1926439351759519 chr7 159138663 2914850 0.018316416294134632 0.32801000683832643 chr8 146364022 6091450 0.041618492828790946 0.31325978502703977 chr9 141213431 2455840 0.017390980323960827 0.25571646206802345 chr10 135534747 3240770 0.023910990146312813 0.3794891317775923 chr11 135006516 2076895 0.015383664889182089 0.2002477711874924 chr12 133851895 2713898 0.020275379739674214 0.20223288106440254 chr13 115169878 1326050 0.011513861289320807 0.14632137219580355 chr14 107349540 1316903 0.012267430302915132 0.16330381647181577 chr15 102531392 1488705 0.014519504426507738 0.16581344980804189 chr16 90354753 1867529 0.020668851809046502 0.2984396950617005 chr17 81195210 1932285 0.02379801714904118 0.2285156227512676 chr18 78077248 1270495 0.016272282035350426 0.3181522366870701 chr19 59128983 1248350 0.021112319824611224 0.48417405611116743 chr20 63025520 1787313 0.02835856015150688 0.24399210387417886 chr21 48129895 823524 0.017110446636129168 0.19900663122992948 chr22 51304566 466164 0.00908620881813911 0.1363179296948688 chrMT 16571 21660 1.3071027698992215 1.7546888248122405 chrX 155270560 3236385 0.020843519853345024 0.2447699100698652 chrY 59373566 252162 0.0042470415201269875 0.27949516722912