BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124839.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 97,500,404 number of mapped reads = 94,079,843 (96.49%) number of supplementary alignments = 1,734,341 (1.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 48,367,044 number of mapped paired reads (second in pair) = 45,712,799 number of mapped paired reads (both in pair) = 91,267,338 number of mapped paired reads (singletons) = 2,812,505 number of mapped bases = 12,656,802,049 bp number of sequenced bases = 12,648,444,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,856,546 duplication rate = 19.2% >>>>>>> Insert size mean insert size = 117,713.8308 std insert size = 3,309,130.1489 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 53.4739 >>>>>>> ACTG content number of A's = 3,692,566,295 bp (29.19%) number of C's = 2,448,303,240 bp (19.36%) number of T's = 3,733,979,412 bp (29.52%) number of G's = 2,773,369,443 bp (21.93%) number of N's = 226,120 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 165,147,072 number of insertions = 1,968,651 mapped reads with insertion percentage = 1.98% number of deletions = 4,427,753 mapped reads with deletion percentage = 4.53% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 4.0885X std coverageData = 37.4067X There is a 49.1% of reference with a coverageData >= 1X There is a 40.22% of reference with a coverageData >= 2X There is a 33.6% of reference with a coverageData >= 3X There is a 28.69% of reference with a coverageData >= 4X There is a 24.7% of reference with a coverageData >= 5X There is a 21.46% of reference with a coverageData >= 6X There is a 18.75% of reference with a coverageData >= 7X There is a 16.48% of reference with a coverageData >= 8X There is a 14.55% of reference with a coverageData >= 9X There is a 12.9% of reference with a coverageData >= 10X There is a 11.47% of reference with a coverageData >= 11X There is a 10.23% of reference with a coverageData >= 12X There is a 9.16% of reference with a coverageData >= 13X There is a 8.22% of reference with a coverageData >= 14X There is a 7.39% of reference with a coverageData >= 15X There is a 6.66% of reference with a coverageData >= 16X There is a 6.02% of reference with a coverageData >= 17X There is a 5.45% of reference with a coverageData >= 18X There is a 4.94% of reference with a coverageData >= 19X There is a 4.49% of reference with a coverageData >= 20X There is a 4.08% of reference with a coverageData >= 21X There is a 3.72% of reference with a coverageData >= 22X There is a 3.4% of reference with a coverageData >= 23X There is a 3.1% of reference with a coverageData >= 24X There is a 2.84% of reference with a coverageData >= 25X There is a 2.61% of reference with a coverageData >= 26X There is a 2.39% of reference with a coverageData >= 27X There is a 2.2% of reference with a coverageData >= 28X There is a 2.02% of reference with a coverageData >= 29X There is a 1.87% of reference with a coverageData >= 30X There is a 1.72% of reference with a coverageData >= 31X There is a 1.59% of reference with a coverageData >= 32X There is a 1.47% of reference with a coverageData >= 33X There is a 1.36% of reference with a coverageData >= 34X There is a 1.26% of reference with a coverageData >= 35X There is a 1.17% of reference with a coverageData >= 36X There is a 1.09% of reference with a coverageData >= 37X There is a 1.01% of reference with a coverageData >= 38X There is a 0.94% of reference with a coverageData >= 39X There is a 0.88% of reference with a coverageData >= 40X There is a 0.82% of reference with a coverageData >= 41X There is a 0.76% of reference with a coverageData >= 42X There is a 0.71% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.59% of reference with a coverageData >= 46X There is a 0.55% of reference with a coverageData >= 47X There is a 0.52% of reference with a coverageData >= 48X There is a 0.49% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1027947426 4.124151915352701 41.34814448367672 chr2 243199373 1147278345 4.717439567576517 40.51171641456642 chr3 198022430 930400671 4.698461032924402 9.250504765474817 chr4 191154276 597509044 3.125794810888771 30.869633826238076 chr5 180915260 724488390 4.004573135511068 8.475912694279176 chr6 171115067 638609002 3.7320442506678853 21.123324072187422 chr7 159138663 910130839 5.7191057273115335 51.794449863785275 chr8 146364022 1172921816 8.013730423450648 23.429160870175497 chr9 141213431 654851130 4.637314774966413 69.14569434909548 chr10 135534747 692217481 5.107306401656543 89.07909948813278 chr11 135006516 444650640 3.2935494757897463 21.17584254614314 chr12 133851895 729501560 5.450065238149971 19.835737187041705 chr13 115169878 287918415 2.499945471853326 5.727090979614082 chr14 107349540 280574095 2.6136497184803957 6.595281885113252 chr15 102531392 272937032 2.6619850435659744 11.642563706337397 chr16 90354753 425340711 4.707452534345371 39.38308158724748 chr17 81195210 279680040 3.4445386618250016 60.37079436021781 chr18 78077248 219873385 2.8161006007793716 46.63022614584036 chr19 59128983 138899707 2.3490968380092045 26.669539033974733 chr20 63025520 203699560 3.23201712576112 11.657809278067305 chr21 48129895 124860143 2.594232607405439 15.688590830237988 chr22 51304566 102164849 1.991340283435981 6.777066978171704 chrMT 16571 5236724 316.0173797598214 185.31998305441732 chrX 155270560 491091119 3.162808963914344 14.35690564887345 chrY 59373566 154019925 2.5940824406605456 43.88436479100156