BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975339.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,512,670 number of mapped reads = 4,446,496 (98.53%) number of supplementary alignments = 19,004 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,222,848 number of mapped paired reads (second in pair) = 2,223,648 number of mapped paired reads (both in pair) = 4,434,424 number of mapped paired reads (singletons) = 12,072 number of mapped bases = 403,314,366 bp number of sequenced bases = 403,085,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,352 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 86,047.6935 std insert size = 2,828,657.9394 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.0984 >>>>>>> ACTG content number of A's = 115,372,820 bp (28.62%) number of C's = 78,664,563 bp (19.52%) number of T's = 120,345,331 bp (29.86%) number of G's = 88,694,791 bp (22%) number of N's = 8,265 bp (0%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 3,064,672 number of insertions = 63,497 mapped reads with insertion percentage = 1.4% number of deletions = 142,468 mapped reads with deletion percentage = 3.14% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.1303X std coverageData = 0.8418X There is a 9.21% of reference with a coverageData >= 1X There is a 2.65% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% 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 0.01% 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 32574689 0.1306905028734111 0.9670177045166016 chr2 243199373 35459410 0.1458038709663943 1.1725404041709773 chr3 198022430 23766631 0.12001989370598068 0.44063456740001045 chr4 191154276 24097305 0.12606207668616318 0.5956834827006559 chr5 180915260 24600070 0.13597564959418018 0.4774701801247487 chr6 171115067 34654543 0.2025218679311273 1.129158530039851 chr7 159138663 20987171 0.13187977455861874 0.8639921712835253 chr8 146364022 20136042 0.13757507975559732 0.5180397668604517 chr9 141213431 16696399 0.11823520526174312 1.0233616152775493 chr10 135534747 19996429 0.1475372879841654 1.4874043651550795 chr11 135006516 18875047 0.1398084148768049 0.6965025040244402 chr12 133851895 17853989 0.13338615041647336 0.4639630590646407 chr13 115169878 12304028 0.1068337330356467 0.41377489473047735 chr14 107349540 12181606 0.11347608941780281 0.4632328112706871 chr15 102531392 12061251 0.11763471425414765 0.441696491360471 chr16 90354753 12352380 0.13670979765724112 0.949742741554287 chr17 81195210 9447614 0.11635679001261282 1.3924922995451479 chr18 78077248 16228457 0.2078512936316608 1.256717167052925 chr19 59128983 5660203 0.09572637161711373 0.6012428447138991 chr20 63025520 9253130 0.14681560739205324 0.5029805829811879 chr21 48129895 4900068 0.10180923935113509 0.5190621999570102 chr22 51304566 4543617 0.08856164965901865 0.3954995136691856 chrMT 16571 96245 5.808038138917386 6.7736865991655835 chrX 155270560 11938145 0.07688608194624919 0.4174938475637242 chrY 59373566 2649897 0.044630922117765336 0.8823103196897996