BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080642.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,662,902 number of mapped reads = 3,098,749 (84.6%) number of supplementary alignments = 18,938 (0.52%) number of secondary alignments = 0 number of mapped bases = 202,993,223 bp number of sequenced bases = 202,910,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,153 duplication rate = 4.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0644 >>>>>>> ACTG content number of A's = 54,349,368 bp (26.78%) number of C's = 35,337,486 bp (17.42%) number of T's = 66,594,420 bp (32.82%) number of G's = 46,470,035 bp (22.9%) number of N's = 159,105 bp (0.08%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,780,003 number of insertions = 17,796 mapped reads with insertion percentage = 0.57% number of deletions = 50,992 mapped reads with deletion percentage = 1.63% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 0.0656X std coverageData = 0.4802X There is a 5.41% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 27631963 0.11086015709465374 0.777956203093535 chr2 243199373 13737627 0.056487098755801476 0.5074898658367147 chr3 198022430 12494363 0.06309569577547351 0.28948759150858244 chr4 191154276 7089267 0.03708662525550828 0.23297503745133014 chr5 180915260 9758395 0.05393903753613708 0.26686631822298684 chr6 171115067 10835617 0.06332357044865021 0.446554011677552 chr7 159138663 11511573 0.0723367457221882 1.0251003909462528 chr8 146364022 23022443 0.15729577996975241 0.6631956895991726 chr9 141213431 5702007 0.04037864500296717 0.37456900399235366 chr10 135534747 9967718 0.07354363527162522 0.42869386045845975 chr11 135006516 8510844 0.06304024614634156 0.35758540339585093 chr12 133851895 6597806 0.049291838565303836 0.2588633285244755 chr13 115169878 3390870 0.029442333871361748 0.1951298716374078 chr14 107349540 4681475 0.0436096419230115 0.25916497633779356 chr15 102531392 4501124 0.043899959926419416 0.2414700462340248 chr16 90354753 5413593 0.05991486690246389 0.3031717373109791 chr17 81195210 3779586 0.04654937157007168 0.28929524351569963 chr18 78077248 5730723 0.07339811720822947 0.6145517363900774 chr19 59128983 4144707 0.07009603057099764 0.5020940695460134 chr20 63025520 5912309 0.09380817484726822 0.3660543668879156 chr21 48129895 2894292 0.060135015877346085 0.29615711087381763 chr22 51304566 2370247 0.04619953319554443 0.24597616787807125 chrMT 16571 195964 11.825719630680103 8.153391226049699 chrX 155270560 12693968 0.08175386241925063 0.3920803560619563 chrY 59373566 424742 0.007153722247371835 0.14022294435054952