BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472502.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 = 16,065,464 number of mapped reads = 15,904,160 (99%) number of supplementary alignments = 71,321 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,973,171 number of mapped paired reads (second in pair) = 7,930,989 number of mapped paired reads (both in pair) = 15,818,054 number of mapped paired reads (singletons) = 86,106 number of mapped bases = 1,565,233,336 bp number of sequenced bases = 1,565,044,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,276,196 duplication rate = 45.98% >>>>>>> Insert size mean insert size = 37,353.3059 std insert size = 1,887,497.1738 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.9995 >>>>>>> ACTG content number of A's = 435,011,312 bp (27.8%) number of C's = 349,439,842 bp (22.33%) number of T's = 433,492,475 bp (27.7%) number of G's = 346,857,210 bp (22.16%) number of N's = 243,532 bp (0.02%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 9,175,015 number of insertions = 81,305 mapped reads with insertion percentage = 0.51% number of deletions = 75,603 mapped reads with deletion percentage = 0.47% homopolymer indels = 44.54% >>>>>>> Coverage mean coverageData = 0.5056X std coverageData = 19.7378X There is a 4.78% of reference with a coverageData >= 1X There is a 2.16% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% 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 0.31% 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 0.22% 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 0.19% 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 0.18% 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 0.17% 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 0.16% of reference with a coverageData >= 37X There is a 0.16% 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 0.15% 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 0.14% of reference with a coverageData >= 47X There is a 0.14% 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 120453624 0.4832630848289842 18.50354932851365 chr2 243199373 137737321 0.566355576089417 23.250603031758523 chr3 198022430 199092208 1.00540230720328 30.73314205622057 chr4 191154276 56175269 0.29387398584795454 11.3447007651506 chr5 180915260 117360437 0.6487039125389422 22.694359490878693 chr6 171115067 95218199 0.5564571295174141 20.821445515692044 chr7 159138663 62353995 0.3918217850051939 15.11812808886496 chr8 146364022 63181539 0.4316739738130454 15.376443515507743 chr9 141213431 80013014 0.5666105088828272 15.57650255262293 chr10 135534747 36363347 0.26829538406118103 9.508855682896751 chr11 135006516 65123270 0.4823713101373566 20.81080990145743 chr12 133851895 54555106 0.40757813701479534 12.840362704212398 chr13 115169878 47384344 0.4114300095030056 22.3693067504729 chr14 107349540 36299503 0.33814306982591635 17.34283054549867 chr15 102531392 30498322 0.2974535057516824 9.453688774637783 chr16 90354753 84065273 0.930391265637127 29.383240588055948 chr17 81195210 55137288 0.6790706988749706 17.137206625578713 chr18 78077248 23815295 0.3050222133853898 11.775378974397867 chr19 59128983 30376548 0.5137336456471778 21.735650453093907 chr20 63025520 28682812 0.4550983791962367 18.706924300946202 chr21 48129895 6813060 0.14155567968722974 5.949073862265805 chr22 51304566 15110466 0.2945247797242842 10.269943466704166 chrMT 16571 1518 0.0916058173918291 0.43191355691694777 chrX 155270560 114213917 0.7355799901797224 30.12539166385658 chrY 59373566 5207661 0.08771009307407947 6.173088982623845