BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472687.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 = 17,016,572 number of mapped reads = 16,897,459 (99.3%) number of supplementary alignments = 99,019 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,473,718 number of mapped paired reads (second in pair) = 8,423,741 number of mapped paired reads (both in pair) = 16,817,498 number of mapped paired reads (singletons) = 79,961 number of mapped bases = 1,661,076,025 bp number of sequenced bases = 1,660,856,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,836,395 duplication rate = 49.39% >>>>>>> Insert size mean insert size = 18,874.5669 std insert size = 1,342,117.8956 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.7743 >>>>>>> ACTG content number of A's = 443,417,270 bp (26.7%) number of C's = 389,528,423 bp (23.45%) number of T's = 444,603,225 bp (26.77%) number of G's = 383,005,645 bp (23.06%) number of N's = 301,882 bp (0.02%) GC percentage = 46.51% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,351,952 number of insertions = 96,146 mapped reads with insertion percentage = 0.56% number of deletions = 89,867 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.5366X std coverageData = 24.0272X There is a 3.3% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 202637020 0.8129850155919972 29.162362536188812 chr2 243199373 99193877 0.4078706115743152 15.968298451712524 chr3 198022430 177441312 0.896066733450347 33.374744461693595 chr4 191154276 24405425 0.12767396843374826 6.206789063253666 chr5 180915260 60718812 0.3356201793038354 20.66440684833382 chr6 171115067 113782674 0.6649483063931477 22.106975825748766 chr7 159138663 82018916 0.5153927678781617 21.482291940251184 chr8 146364022 85598863 0.5848354112597425 21.967033726385026 chr9 141213431 94159096 0.6667856968930951 20.03962249732934 chr10 135534747 27594624 0.2035981518451501 9.700720896172063 chr11 135006516 46186702 0.3421072061440353 12.971294734286525 chr12 133851895 87682121 0.6550682080369501 23.78136206092885 chr13 115169878 58413248 0.5071920628412926 27.630339757411335 chr14 107349540 19284621 0.17964325697157155 9.438849618697967 chr15 102531392 32225220 0.31429613283705343 18.518884181597848 chr16 90354753 125716644 1.3913672477196635 56.25917509334206 chr17 81195210 38449928 0.4735492155263839 14.04783065648769 chr18 78077248 32746171 0.41940734130383284 32.55073867259466 chr19 59128983 53177702 0.8993508648711241 27.45268458538007 chr20 63025520 100651543 1.5969966293019082 52.061785351791904 chr21 48129895 10131942 0.2105124476170164 15.414943993255092 chr22 51304566 19914785 0.3881678874352041 24.987963543847318 chrMT 16571 2812 0.16969404381147787 0.6414757830994612 chrX 155270560 67957933 0.4376742957583202 15.191158095366195 chrY 59373566 984034 0.016573604489243582 0.7808563488308136