BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093994.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 349,426 number of mapped reads = 329,386 (94.26%) number of supplementary alignments = 20,336 (5.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 165,582 number of mapped paired reads (second in pair) = 163,804 number of mapped paired reads (both in pair) = 326,412 number of mapped paired reads (singletons) = 2,974 number of mapped bases = 41,443,326 bp number of sequenced bases = 40,673,873 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,016 duplication rate = 50.17% >>>>>>> Insert size mean insert size = 1,071,446.404 std insert size = 9,440,421.2808 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 40.5771 >>>>>>> ACTG content number of A's = 10,664,706 bp (26.22%) number of C's = 9,565,633 bp (23.52%) number of T's = 10,074,851 bp (24.77%) number of G's = 10,368,128 bp (25.49%) number of N's = 555 bp (0%) GC percentage = 49.01% >>>>>>> Mismatches and indels general error rate = 0.036 number of mismatches = 1,418,389 number of insertions = 22,934 mapped reads with insertion percentage = 6.83% number of deletions = 112,460 mapped reads with deletion percentage = 32.79% homopolymer indels = 29.69% >>>>>>> Coverage mean coverageData = 0.0134X std coverageData = 2.5253X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 725368 0.0029101953571461715 1.0284271788050408 chr2 243199373 1813197 0.007455598991202991 2.3912497458448314 chr3 198022430 815084 0.004116119572919088 1.3551757467050858 chr4 191154276 905233 0.004735614703173054 1.4582424472373858 chr5 180915260 368626 0.002037561673901914 1.0657377864692215 chr6 171115067 722189 0.004220487492197282 1.1373564762074242 chr7 159138663 913952 0.0057431172461213905 1.6941671873288713 chr8 146364022 453554 0.003098807984382938 0.953102801129898 chr9 141213431 648819 0.004594598370745627 1.5123928893239997 chr10 135534747 653690 0.004823043643561013 1.3330039319929723 chr11 135006516 962833 0.007131752070396365 1.6956294661802584 chr12 133851895 940980 0.00703000880189257 1.784488365288613 chr13 115169878 846345 0.0073486662892878985 1.8791289750816227 chr14 107349540 198659 0.001850580822237338 0.6194810627928342 chr15 102531392 634982 0.006193049636934608 1.724119863060989 chr16 90354753 268595 0.0029726715095995007 0.9092014280887815 chr17 81195210 917778 0.011303351515440381 2.722556812855817 chr18 78077248 228430 0.0029256922580058148 0.8405740211132446 chr19 59128983 147418 0.0024931597419830475 0.7451089196870876 chr20 63025520 309090 0.004904203884394766 1.5645548140175483 chr21 48129895 102571 0.0021311286883131577 0.40881342775818413 chr22 51304566 153994 0.0030015652018184893 0.7353299337647158 chrMT 16571 737611 44.51215979723614 189.42222741949428 chrX 155270560 26397660 0.17001072192951452 8.955845314409231 chrY 59373566 576668 0.009712537731016527 1.483922523457734