BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617493.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,488,491 (95.28%) number of supplementary alignments = 158,747 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,376,185 number of mapped paired reads (second in pair) = 15,112,306 number of mapped paired reads (both in pair) = 29,941,990 number of mapped paired reads (singletons) = 546,501 number of mapped bases = 2,968,653,649 bp number of sequenced bases = 2,966,883,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,272,564 duplication rate = 9.93% >>>>>>> Insert size mean insert size = 39,444.6599 std insert size = 1,865,041.3775 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 52.6954 >>>>>>> ACTG content number of A's = 875,567,341 bp (29.51%) number of C's = 599,357,861 bp (20.2%) number of T's = 875,250,237 bp (29.5%) number of G's = 613,658,919 bp (20.68%) number of N's = 3,049,169 bp (0.1%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 34,346,854 number of insertions = 445,024 mapped reads with insertion percentage = 1.43% number of deletions = 1,036,164 mapped reads with deletion percentage = 3.33% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.959X std coverageData = 9.6736X There is a 38.17% of reference with a coverageData >= 1X There is a 20.61% of reference with a coverageData >= 2X There is a 11.63% of reference with a coverageData >= 3X There is a 6.91% of reference with a coverageData >= 4X There is a 4.26% of reference with a coverageData >= 5X There is a 2.73% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.24% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191510921 0.7683468158741318 9.356098590904036 chr2 243199373 307007082 1.2623679009238236 11.453872021701049 chr3 198022430 245222586 1.2383576244367873 2.2522647047934607 chr4 191154276 153344543 0.8022030488085968 6.135219418437087 chr5 180915260 189790476 1.0490573100356488 2.091778936886702 chr6 171115067 139857499 0.8173301244127147 5.424455067500257 chr7 159138663 229104144 1.4396510545020729 13.185633112517834 chr8 146364022 131796793 0.9004726106802394 3.8632975504688103 chr9 141213431 122781768 0.8694765585010111 18.16104263070223 chr10 135534747 126099886 0.9303878805336907 18.615797965938107 chr11 135006516 167483870 1.240561381496579 12.717036299618764 chr12 133851895 129597891 0.9682185747164804 1.9962610722229914 chr13 115169878 125858464 1.0928071313924637 2.1254087606466396 chr14 107349540 86462110 0.8054259943731478 2.2380428936688004 chr15 102531392 67063961 0.6540822248858184 1.4977865215643407 chr16 90354753 80004331 0.8854468452810668 14.77267479721429 chr17 81195210 82797991 1.0197398467224852 13.573278605110193 chr18 78077248 53087741 0.6799386807280913 16.93811016636627 chr19 59128983 35612817 0.602290369174792 5.902453062281073 chr20 63025520 87575568 1.3895255128398782 2.7981343430186576 chr21 48129895 42512620 0.8832892737455588 3.755814881200318 chr22 51304566 22210567 0.4329159903623393 1.2608757327616669 chrMT 16571 2063310 124.51330637861324 90.99569247154882 chrX 155270560 139516719 0.8985394204799674 4.188272754308091 chrY 59373566 10289991 0.17330929727212274 13.723904195013144