BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472634.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 = 16,321,258 number of mapped reads = 16,179,238 (99.13%) number of supplementary alignments = 71,366 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,107,152 number of mapped paired reads (second in pair) = 8,072,086 number of mapped paired reads (both in pair) = 16,087,152 number of mapped paired reads (singletons) = 92,086 number of mapped bases = 1,590,060,795 bp number of sequenced bases = 1,589,858,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,825,863 duplication rate = 49.65% >>>>>>> Insert size mean insert size = 20,860.6961 std insert size = 1,472,838.0011 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 54.8387 >>>>>>> ACTG content number of A's = 419,597,427 bp (26.39%) number of C's = 377,368,644 bp (23.74%) number of T's = 419,650,220 bp (26.4%) number of G's = 372,946,651 bp (23.46%) number of N's = 295,544 bp (0.02%) GC percentage = 47.19% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 10,110,156 number of insertions = 106,214 mapped reads with insertion percentage = 0.65% number of deletions = 84,138 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.63% >>>>>>> Coverage mean coverageData = 0.5136X std coverageData = 20.323X There is a 3.17% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.55% 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 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 239881310 0.9624100796121988 28.241701807933723 chr2 243199373 97283909 0.400017104484887 14.51504595672456 chr3 198022430 136212470 0.6878638445149875 24.650661834317035 chr4 191154276 22787398 0.1192094599024298 5.206340930122089 chr5 180915260 73161119 0.4043944054249487 17.490451789823506 chr6 171115067 158994722 0.9291684524776536 30.311506890878032 chr7 159138663 65636648 0.412449412120548 13.764902417390223 chr8 146364022 68503669 0.4680362568883219 13.95168584343225 chr9 141213431 81134369 0.5745513611945311 22.15903764206656 chr10 135534747 35404955 0.2612241936748515 9.94458103965978 chr11 135006516 33751025 0.24999552614186416 8.391279116251006 chr12 133851895 62110328 0.46402277681612203 18.265417386046963 chr13 115169878 44577015 0.38705446054219145 13.452127495056713 chr14 107349540 28666420 0.26703812610654876 13.089135760921858 chr15 102531392 15878683 0.15486655052922718 6.292037418815427 chr16 90354753 79984746 0.8852300885599234 33.83125204677472 chr17 81195210 64792195 0.7979805089487422 18.732647815467406 chr18 78077248 15839439 0.2028688178148902 10.924255071756432 chr19 59128983 49563693 0.838230094368442 22.798954237108774 chr20 63025520 80810704 1.2821901985100639 46.90610129121909 chr21 48129895 11738112 0.24388401429091006 17.840348919165383 chr22 51304566 31391465 0.6118649361540257 18.37775611290187 chrMT 16571 3384 0.20421217790115262 0.564095068256379 chrX 155270560 90777068 0.5846379893265021 26.372097161942637 chrY 59373566 1175949 0.019805935186712552 1.4643949027368441