BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038411.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,397,660 number of mapped reads = 14,083,609 (97.82%) number of supplementary alignments = 269,940 (1.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,108,793 number of mapped paired reads (second in pair) = 6,974,816 number of mapped paired reads (both in pair) = 13,931,422 number of mapped paired reads (singletons) = 152,187 number of mapped bases = 2,013,979,527 bp number of sequenced bases = 2,012,385,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,966,448 duplication rate = 8.72% >>>>>>> Insert size mean insert size = 106,307.3562 std insert size = 3,102,667.583 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 53.7808 >>>>>>> ACTG content number of A's = 581,458,337 bp (28.89%) number of C's = 415,000,971 bp (20.62%) number of T's = 582,618,888 bp (28.95%) number of G's = 433,264,501 bp (21.53%) number of N's = 43,268 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 26,807,731 number of insertions = 392,626 mapped reads with insertion percentage = 2.55% number of deletions = 736,934 mapped reads with deletion percentage = 4.98% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.6506X std coverageData = 8.2178X There is a 27.61% of reference with a coverageData >= 1X There is a 14.48% of reference with a coverageData >= 2X There is a 7.53% of reference with a coverageData >= 3X There is a 4.36% of reference with a coverageData >= 4X There is a 2.52% of reference with a coverageData >= 5X There is a 1.53% of reference with a coverageData >= 6X There is a 0.95% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 132865685 0.5330605976704869 5.213485930205214 chr2 243199373 184845329 0.7600567662647716 11.03585424645804 chr3 198022430 140284696 0.7084283128936454 1.5247133043528374 chr4 191154276 101072752 0.528749626296615 6.947051131870754 chr5 180915260 115644950 0.6392216444317632 1.677300217401645 chr6 171115067 147696291 0.8631401874155243 9.064379144784063 chr7 159138663 153190637 0.9626236271697218 8.448629012839675 chr8 146364022 116543994 0.7962612150682769 2.3466774665488424 chr9 141213431 84480068 0.5982438596793247 10.722636618534397 chr10 135534747 91422061 0.6745285841718508 21.85958813747392 chr11 135006516 93600324 0.6933022699437708 3.415449064126389 chr12 133851895 73570335 0.5496398463391198 1.419584351925099 chr13 115169878 114357555 0.9929467408136006 1.964540881827631 chr14 107349540 40080292 0.3733624941476228 1.3536974541212958 chr15 102531392 39759184 0.38777571653372267 1.0394984685636712 chr16 90354753 83295362 0.921870286115441 18.975702651913533 chr17 81195210 38452295 0.4735783674923681 3.5537849041391225 chr18 78077248 33134559 0.42438174818866564 9.425569236948633 chr19 59128983 26663574 0.45093916125700995 3.353561731616072 chr20 63025520 65463308 1.0386793794005984 2.849641422707528 chr21 48129895 18534681 0.3850970586991723 3.2917922093157257 chr22 51304566 14648670 0.28552370952714035 1.4828695804350702 chrMT 16571 945729 57.07132943093356 25.732781308064816 chrX 155270560 75945418 0.48911666190937936 1.5765756657484646 chrY 59373566 27481778 0.4628621767471403 12.837501379015574