BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082955.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 = 4,333,604 number of mapped reads = 3,594,592 (82.95%) number of supplementary alignments = 23,449 (0.54%) number of secondary alignments = 0 number of mapped bases = 247,797,409 bp number of sequenced bases = 247,698,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,902 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5522 >>>>>>> ACTG content number of A's = 72,078,111 bp (29.1%) number of C's = 45,910,286 bp (18.53%) number of T's = 79,158,913 bp (31.96%) number of G's = 50,525,943 bp (20.4%) number of N's = 25,437 bp (0.01%) GC percentage = 38.93% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,258,652 number of insertions = 21,178 mapped reads with insertion percentage = 0.58% number of deletions = 56,685 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.08X std coverageData = 0.5817X There is a 6.13% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 20123447 0.08073579483679601 1.0582577737994516 chr2 243199373 21181922 0.08709694329680694 0.6114143980362685 chr3 198022430 16174395 0.08167961073904607 0.35661427273727847 chr4 191154276 19006500 0.09943015870594493 0.4053842622882338 chr5 180915260 15120822 0.08357958306004701 0.3632069563142252 chr6 171115067 14533708 0.08493529094080302 0.4289492584788206 chr7 159138663 14371906 0.09031058656060219 0.7565365220362862 chr8 146364022 13789688 0.0942150113912557 0.8950568736806723 chr9 141213431 10920746 0.07733503762825507 0.5331514836608677 chr10 135534747 11029117 0.08137483002790422 0.47585699248619207 chr11 135006516 12083731 0.0895047984202481 0.621785472487059 chr12 133851895 10960599 0.08188602036601723 0.36588842265819915 chr13 115169878 8617482 0.07482409593244511 0.34501274539132837 chr14 107349540 6683421 0.06225849686919944 0.35326146288362476 chr15 102531392 6326750 0.061705492109187396 0.3069409552343217 chr16 90354753 6186788 0.06847219204948743 0.3884607714279448 chr17 81195210 5417864 0.06672639925434025 0.3891161237814511 chr18 78077248 6746683 0.08641035862329574 0.9885128994131598 chr19 59128983 3851807 0.06514245306738999 0.7115745228778142 chr20 63025520 4380092 0.06949711799283846 0.3370850055630746 chr21 48129895 3685943 0.076583233767703 0.38010564844764005 chr22 51304566 2124086 0.0414015002095525 0.24864092048147465 chrMT 16571 65603 3.958904109589041 3.280781256185026 chrX 155270560 13863149 0.08928382173671558 0.41100548031561707 chrY 59373566 551160 0.009282918933991602 0.218706237398298