BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080945.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 = 3,677,099 number of mapped reads = 3,326,729 (90.47%) number of supplementary alignments = 40,387 (1.1%) number of secondary alignments = 0 number of mapped bases = 230,453,558 bp number of sequenced bases = 230,368,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,278 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0798 >>>>>>> ACTG content number of A's = 67,277,379 bp (29.2%) number of C's = 40,916,111 bp (17.76%) number of T's = 73,821,614 bp (32.05%) number of G's = 47,217,382 bp (20.5%) number of N's = 1,136,061 bp (0.49%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 2,684,426 number of insertions = 17,604 mapped reads with insertion percentage = 0.53% number of deletions = 51,227 mapped reads with deletion percentage = 1.52% homopolymer indels = 50.01% >>>>>>> Coverage mean coverageData = 0.0744X std coverageData = 0.4637X There is a 5.42% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% 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% 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 17532749 0.07034184681128638 0.6876763479324923 chr2 243199373 20650374 0.08491129621456714 0.4595425850587136 chr3 198022430 16410943 0.08287416228555523 0.37540382114747867 chr4 191154276 15521814 0.08120045402489454 0.3784509344268601 chr5 180915260 14356145 0.07935286940416193 0.3693038745327487 chr6 171115067 13670945 0.07989328607749077 0.4051231681543289 chr7 159138663 12554607 0.0788909920652029 0.5239870665963114 chr8 146364022 12058018 0.08238375684975369 0.8176328179109835 chr9 141213431 9433775 0.06680508315104956 0.42021278467762174 chr10 135534747 10945896 0.08076081036252644 0.4305628092941049 chr11 135006516 10805392 0.08003607766605872 0.4404309597181702 chr12 133851895 10604514 0.0792257293032721 0.3687105329361404 chr13 115169878 8327658 0.0723076045977925 0.35092173162604035 chr14 107349540 6796399 0.0633109280207442 0.3421940837238628 chr15 102531392 6354056 0.061971810545593684 0.3231110604064864 chr16 90354753 5379209 0.05953432245008738 0.33072783126997524 chr17 81195210 4865153 0.059919211983071416 0.33838553732467636 chr18 78077248 6133298 0.07855422875560368 0.6803384114483656 chr19 59128983 3457520 0.0584742003764888 0.4864823842413329 chr20 63025520 4582586 0.07271000699399227 0.3564850303322438 chr21 48129895 3110214 0.06462125047228963 0.3455819354750375 chr22 51304566 1833141 0.03573056246104879 0.2428108780889473 chrMT 16571 39619 2.3908635568161247 2.1508413838054317 chrX 155270560 14532449 0.09359436199624707 0.4153309742098438 chrY 59373566 497084 0.008372143253110316 0.14291354475728488