BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472433.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 = 15,310,598 number of mapped reads = 15,167,674 (99.07%) number of supplementary alignments = 59,772 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,606,178 number of mapped paired reads (second in pair) = 7,561,496 number of mapped paired reads (both in pair) = 15,087,326 number of mapped paired reads (singletons) = 80,348 number of mapped bases = 1,483,519,548 bp number of sequenced bases = 1,483,328,706 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,181,254 duplication rate = 45.78% >>>>>>> Insert size mean insert size = 19,193.8831 std insert size = 1,355,694.4419 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 54.8107 >>>>>>> ACTG content number of A's = 408,028,639 bp (27.51%) number of C's = 334,477,741 bp (22.55%) number of T's = 408,798,667 bp (27.56%) number of G's = 331,843,920 bp (22.37%) number of N's = 179,739 bp (0.01%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 8,003,725 number of insertions = 97,501 mapped reads with insertion percentage = 0.64% number of deletions = 80,813 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.4792X std coverageData = 15.4187X There is a 4.31% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% 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 142900216 0.5733193980688217 18.37160350534903 chr2 243199373 134709506 0.5539056467879956 18.324219353308468 chr3 198022430 100556599 0.5078040856280776 11.858695444717812 chr4 191154276 34163272 0.17872094056635177 5.852025274217404 chr5 180915260 59361620 0.32811836878768547 10.773549600543268 chr6 171115067 120494081 0.7041699080771187 16.820123950310382 chr7 159138663 93030232 0.5845859846139339 15.341547336041831 chr8 146364022 181227262 1.2381954220962854 32.53592854914353 chr9 141213431 41523956 0.2940510382472047 8.248435067725305 chr10 135534747 21179024 0.15626268885867325 4.340452819193598 chr11 135006516 43107217 0.3192973071018291 9.649528555269452 chr12 133851895 80845000 0.6039884605294531 14.703996555293518 chr13 115169878 52829302 0.4587076318688121 14.152091769346823 chr14 107349540 27753840 0.25853711157029646 9.777096369376277 chr15 102531392 25204277 0.24582009966274523 9.0119335978364 chr16 90354753 75287603 0.8332445222887168 25.46660195987639 chr17 81195210 55719168 0.6862371314761055 15.673705035996125 chr18 78077248 9939765 0.12730680517837925 3.993835079333981 chr19 59128983 24933886 0.42168636656578384 8.457127279944876 chr20 63025520 46606839 0.7394915424735885 19.138182214379746 chr21 48129895 16052113 0.3335164766098077 21.459305511157222 chr22 51304566 14652491 0.28559818632906864 10.00800818811467 chrMT 16571 2980 0.17983223704061313 0.5183320858340292 chrX 155270560 81169434 0.5227612626630573 16.838642518270564 chrY 59373566 269865 0.004545204510707677 0.39234824194710355