BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084822.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 = 2,343,891 number of mapped reads = 2,161,314 (92.21%) number of supplementary alignments = 22,223 (0.95%) number of secondary alignments = 0 number of mapped bases = 145,775,677 bp number of sequenced bases = 145,719,867 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,636 duplication rate = 4.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0661 >>>>>>> ACTG content number of A's = 40,670,510 bp (27.91%) number of C's = 26,566,759 bp (18.23%) number of T's = 46,731,277 bp (32.07%) number of G's = 31,730,142 bp (21.77%) number of N's = 21,179 bp (0.01%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,106,782 number of insertions = 11,818 mapped reads with insertion percentage = 0.54% number of deletions = 34,396 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.3066X There is a 3.75% of reference with a coverageData >= 1X There is a 0.71% 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 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 10590793 0.04249053806770656 0.335199991327509 chr2 243199373 11907178 0.048960562081712275 0.4330204604750457 chr3 198022430 12154307 0.06137843576608973 0.3037340731641832 chr4 191154276 8066600 0.042199422209106115 0.2537049999555388 chr5 180915260 8087521 0.04470336554251974 0.25568348461616136 chr6 171115067 8501910 0.04968533834603822 0.28541372584773933 chr7 159138663 9702416 0.0609683141550586 0.3515607368143536 chr8 146364022 7605106 0.05196021464892513 0.35373387298143294 chr9 141213431 10307374 0.0729914564571411 0.37454939874913146 chr10 135534747 4079770 0.03010128465433296 0.2171394892035716 chr11 135006516 6613351 0.04898542082220683 0.3317373807243859 chr12 133851895 6573919 0.049113380128088586 0.2695591340674236 chr13 115169878 3988454 0.03463105170607197 0.2246459635791565 chr14 107349540 3160293 0.029439278454290535 0.20946202755186258 chr15 102531392 3005938 0.029317245590501688 0.21489552972278894 chr16 90354753 2834047 0.031365776629371116 0.21752058468111113 chr17 81195210 4161852 0.05125735865453147 0.28233693302203683 chr18 78077248 5957954 0.07630845287989658 0.4549948234790843 chr19 59128983 2775612 0.046941649579868475 0.2848753170144052 chr20 63025520 2624515 0.04164209989858077 0.2484172842141356 chr21 48129895 1313503 0.02729079296765555 0.2070712813841302 chr22 51304566 1160643 0.02262260633878084 0.17758085805824778 chrMT 16571 65957 3.9802667310361475 3.0018206374022838 chrX 155270560 10244264 0.06597686000488438 0.32324735885172073 chrY 59373566 292400 0.004924750519448335 0.08730769726538952