BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472695.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,303,046 number of mapped reads = 15,169,653 (99.13%) number of supplementary alignments = 95,118 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,617,819 number of mapped paired reads (second in pair) = 7,551,834 number of mapped paired reads (both in pair) = 15,096,056 number of mapped paired reads (singletons) = 73,597 number of mapped bases = 1,493,270,267 bp number of sequenced bases = 1,493,091,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,356,594 duplication rate = 47.52% >>>>>>> Insert size mean insert size = 18,431.0314 std insert size = 1,294,960.3799 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.7343 >>>>>>> ACTG content number of A's = 400,342,370 bp (26.81%) number of C's = 344,929,221 bp (23.1%) number of T's = 406,722,890 bp (27.24%) number of G's = 340,756,078 bp (22.82%) number of N's = 340,464 bp (0.02%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 5,974,680 number of insertions = 88,325 mapped reads with insertion percentage = 0.58% number of deletions = 76,454 mapped reads with deletion percentage = 0.5% homopolymer indels = 47.32% >>>>>>> Coverage mean coverageData = 0.4824X std coverageData = 38.5506X There is a 2.78% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187216828 0.7511188026287806 49.88811123719579 chr2 243199373 62394005 0.25655495830575187 17.273756361230745 chr3 198022430 110227950 0.5566437600023392 19.885292866583473 chr4 191154276 55542629 0.2905644077770983 21.538680726591323 chr5 180915260 68249506 0.37724571161106035 22.26587976005637 chr6 171115067 111980359 0.6544155401581323 29.91409516674222 chr7 159138663 86337416 0.5425294794640823 32.78147784268352 chr8 146364022 65288668 0.4460704694217818 27.97011203239353 chr9 141213431 48538929 0.34372742490762087 18.975028255511216 chr10 135534747 32432257 0.23929108747294153 14.755874528739438 chr11 135006516 58677018 0.43462359994535377 28.86245481671725 chr12 133851895 47334125 0.35363059297740984 26.733635382455972 chr13 115169878 27911806 0.24235335214994325 15.401547701813948 chr14 107349540 59913293 0.5581141102234811 38.74905052860288 chr15 102531392 48102472 0.4691487266650978 31.36375649388437 chr16 90354753 180756682 2.000522119738405 149.54253159919034 chr17 81195210 58982186 0.72642445287105 33.289459009915745 chr18 78077248 17979686 0.23028073427997872 10.597690586382596 chr19 59128983 19900631 0.3365630523359416 17.76291916936847 chr20 63025520 69986825 1.1104521628698978 77.81422939590699 chr21 48129895 12660814 0.2630550928897726 19.534643048154784 chr22 51304566 16660335 0.3247339622754045 23.521741870210338 chrMT 16571 3172 0.19141874358819624 0.4787954169735146 chrX 155270560 43939924 0.2829894089388227 20.85023454190415 chrY 59373566 2252751 0.037941985832550464 2.5489132438928523