BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472478.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,015,494 number of mapped reads = 14,637,987 (97.49%) number of supplementary alignments = 73,959 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,350,866 number of mapped paired reads (second in pair) = 7,287,121 number of mapped paired reads (both in pair) = 14,528,464 number of mapped paired reads (singletons) = 109,523 number of mapped bases = 1,438,071,465 bp number of sequenced bases = 1,437,906,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,509,136 duplication rate = 43.8% >>>>>>> Insert size mean insert size = 40,634.0761 std insert size = 1,932,113.9429 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 54.7478 >>>>>>> ACTG content number of A's = 415,570,068 bp (28.9%) number of C's = 304,872,012 bp (21.2%) number of T's = 413,099,300 bp (28.73%) number of G's = 304,143,368 bp (21.15%) number of N's = 221,678 bp (0.02%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 8,948,924 number of insertions = 78,476 mapped reads with insertion percentage = 0.53% number of deletions = 71,648 mapped reads with deletion percentage = 0.48% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.4645X std coverageData = 22.4934X There is a 4.5% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 121965454 0.4893285862665915 18.283516882487646 chr2 243199373 105064373 0.4320092264382606 29.708707591240994 chr3 198022430 130810190 0.6605826925767955 23.360838678659867 chr4 191154276 45896832 0.24010361138874026 10.403916844738756 chr5 180915260 71331517 0.3942813723950097 16.939494202767886 chr6 171115067 87974255 0.5141233705621026 18.39556231226623 chr7 159138663 58835333 0.3697111179072807 15.496415803799417 chr8 146364022 68038117 0.46485547520687837 24.295556514447934 chr9 141213431 111822153 0.7918662708506813 38.13899349989626 chr10 135534747 45313583 0.33433185218547684 17.1069735482427 chr11 135006516 68007834 0.5037374196072136 19.180160045365092 chr12 133851895 89363528 0.6676299054264416 27.57285950030606 chr13 115169878 27207868 0.23624118104909342 9.35898586866234 chr14 107349540 35775962 0.3332660950386932 14.026285943605593 chr15 102531392 38490662 0.3754036812452522 17.495429707683662 chr16 90354753 65272453 0.7224019858700738 24.363055116332543 chr17 81195210 75013872 0.9238706569020513 41.182087311470546 chr18 78077248 26726318 0.3423060966493081 22.166698093510327 chr19 59128983 21679944 0.36665511395655154 12.830266286432929 chr20 63025520 20094554 0.3188320223300022 10.823174720139257 chr21 48129895 5758386 0.11964260466389964 6.080168096119036 chr22 51304566 7344737 0.14315951917418032 6.879815281755379 chrMT 16571 8473 0.5113149478003741 1.4281544577629746 chrX 155270560 106650204 0.6868668728959308 35.33045057108802 chrY 59373566 3624863 0.06105179870786269 4.278644057747125