BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818965.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,585,537 number of mapped reads = 1,560,364 (98.41%) number of supplementary alignments = 26,231 (1.65%) number of secondary alignments = 0 number of mapped bases = 144,389,051 bp number of sequenced bases = 144,303,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 614,438 duplication rate = 33.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2306 >>>>>>> ACTG content number of A's = 42,423,222 bp (29.4%) number of C's = 29,991,411 bp (20.78%) number of T's = 40,280,677 bp (27.91%) number of G's = 31,600,959 bp (21.9%) number of N's = 6,922 bp (0%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 903,534 number of insertions = 22,679 mapped reads with insertion percentage = 1.42% number of deletions = 45,995 mapped reads with deletion percentage = 2.88% homopolymer indels = 41.82% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.559X There is a 2.47% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 14369214 0.057649661783590905 1.0355002221446452 chr2 243199373 11532761 0.04742101452703992 0.7471726429057463 chr3 198022430 7949807 0.04014599255245984 0.33250444942170154 chr4 191154276 8002603 0.04186462980299745 0.3895296891953507 chr5 180915260 7867470 0.04348704470811362 0.3565003369310117 chr6 171115067 6167011 0.03604014017070747 0.36285232291684 chr7 159138663 6986495 0.043901933498083995 0.6645795896843563 chr8 146364022 13470365 0.09203330720168376 0.5564462874771726 chr9 141213431 6120395 0.04334145099838273 0.47143345633979744 chr10 135534747 7642525 0.05638793865900676 0.655374879373987 chr11 135006516 4703649 0.034840162825918716 0.3519333595471826 chr12 133851895 6648079 0.04966742532856931 0.3830369958024229 chr13 115169878 3017970 0.026204508091950917 0.27032394043578745 chr14 107349540 3366423 0.03135945435816492 0.31488796670170305 chr15 102531392 3703452 0.03612017673572597 0.31648030292328116 chr16 90354753 5334610 0.05904072362413519 0.5922066581513032 chr17 81195210 4863048 0.059893286808421334 0.44354501574918725 chr18 78077248 3390037 0.04341901241191288 0.5669862555431748 chr19 59128983 2837957 0.047996039438053584 0.959930079516605 chr20 63025520 4046468 0.06420364322261839 0.44536979190312026 chr21 48129895 1972432 0.040981431602956954 0.377086311623221 chr22 51304566 1086460 0.021176672657166617 0.2639678650692388 chrMT 16571 13227 0.7982016776295938 1.4902084624124108 chrX 155270560 8755245 0.05638702533178215 0.4511557402273479 chrY 59373566 541348 0.009117660205890278 0.49577991763330265