BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549098.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,952,344 number of mapped reads = 10,191,882 (85.27%) number of secondary alignments = 0 number of mapped bases = 404,637,458 bp number of sequenced bases = 404,598,192 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 486,559 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5428 >>>>>>> ACTG content number of A's = 121,372,485 bp (30%) number of C's = 81,269,062 bp (20.09%) number of T's = 121,307,491 bp (29.98%) number of G's = 80,647,639 bp (19.93%) number of N's = 1,515 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,219,597 number of insertions = 9,860 mapped reads with insertion percentage = 0.1% number of deletions = 30,889 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.1307X std coverageData = 1.1565X There is a 10.14% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.46% 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 0.01% 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% 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 32516324 0.1304563409693571 1.9332311463932481 chr2 243199373 35467863 0.14583862845731926 0.7154598184503608 chr3 198022430 28595187 0.14440377789526165 0.46589949674152176 chr4 191154276 28508604 0.1491392429013725 0.5284043713413498 chr5 180915260 26150719 0.14454678394735745 0.4774891812217325 chr6 171115067 24462244 0.14295786121510853 0.5402802523700266 chr7 159138663 22865030 0.14367991768285748 1.1940717680401909 chr8 146364022 21678077 0.14811069485368475 3.6278352096212716 chr9 141213431 17275734 0.12233775411915315 0.6780575211168505 chr10 135534747 19054913 0.1405906117934466 0.7770203760570125 chr11 135006516 18656768 0.13819161143303632 0.701247565322084 chr12 133851895 18665286 0.1394473047990841 0.4885968023271773 chr13 115169878 13858226 0.12032856368919657 0.41864148500981213 chr14 107349540 12534266 0.11676124555354406 0.5779602131090281 chr15 102531392 11561977 0.11276523974238056 0.402544147566377 chr16 90354753 10614888 0.1174801285771873 0.4914929394334448 chr17 81195210 9660548 0.11897928461543483 0.4761345293674926 chr18 78077248 11203278 0.14348966295533366 1.4460718582059393 chr19 59128983 6588284 0.11142224448541589 1.4281419361797234 chr20 63025520 7994228 0.12684112721323046 0.48382910884076125 chr21 48129895 5435540 0.11293479863191058 0.5153994744923402 chr22 51304566 3974208 0.07746304685629735 0.3633660308064994 chrMT 16571 158945 9.591756683362501 11.596045757889383 chrX 155270560 13470212 0.08675316170689408 0.486288377144195 chrY 59373566 3686109 0.06208333520004508 0.6579514164187343