BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038455.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,820,854 number of mapped reads = 17,818,694 (94.68%) number of supplementary alignments = 371,931 (1.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,020,746 number of mapped paired reads (second in pair) = 8,797,948 number of mapped paired reads (both in pair) = 17,517,442 number of mapped paired reads (singletons) = 301,252 number of mapped bases = 2,351,140,998 bp number of sequenced bases = 2,349,176,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,680,050 duplication rate = 18.4% >>>>>>> Insert size mean insert size = 93,384.2872 std insert size = 2,905,806.5707 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 53.1643 >>>>>>> ACTG content number of A's = 663,606,974 bp (28.25%) number of C's = 474,454,061 bp (20.2%) number of T's = 674,809,464 bp (28.73%) number of G's = 536,123,512 bp (22.82%) number of N's = 182,179 bp (0.01%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0144 number of mismatches = 32,278,729 number of insertions = 502,467 mapped reads with insertion percentage = 2.63% number of deletions = 910,569 mapped reads with deletion percentage = 4.88% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.7595X std coverageData = 11.8062X There is a 24.83% of reference with a coverageData >= 1X There is a 15.71% of reference with a coverageData >= 2X There is a 9.47% of reference with a coverageData >= 3X There is a 6.36% of reference with a coverageData >= 4X There is a 4.16% of reference with a coverageData >= 5X There is a 2.87% of reference with a coverageData >= 6X There is a 1.97% of reference with a coverageData >= 7X There is a 1.39% of reference with a coverageData >= 8X There is a 0.99% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.52% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182451222 0.731999066915063 16.226075110784173 chr2 243199373 206297688 0.8482657066718671 12.912311111793827 chr3 198022430 150457164 0.7597985945329526 2.027516212463292 chr4 191154276 156546395 0.8189531423299158 13.472259156272377 chr5 180915260 136464674 0.7543016216542485 1.9421486123150147 chr6 171115067 130730341 0.7639908237887667 6.848833671422592 chr7 159138663 122005093 0.7666590299303947 10.356048468060536 chr8 146364022 116818781 0.7981386368297532 3.669446670173313 chr9 141213431 97301920 0.6890415402483918 15.877756227764904 chr10 135534747 136696510 1.008571698591801 32.989645901374956 chr11 135006516 106864650 0.7915517944333886 6.535202815915353 chr12 133851895 99356400 0.742286091653764 2.008509742864094 chr13 115169878 68150527 0.5917391611719863 1.6262761134963675 chr14 107349540 67517482 0.6289498958262886 1.9855192672003352 chr15 102531392 62690990 0.6114321553344365 1.6637425224702607 chr16 90354753 85452667 0.9457462298635247 15.463678994660699 chr17 81195210 61747832 0.7604861419780797 11.693735853887322 chr18 78077248 65011445 0.8326554363186571 14.161012899343735 chr19 59128983 41699246 0.7052251515978213 7.646010966139116 chr20 63025520 49408170 0.7839391091100875 4.225386676777041 chr21 48129895 32020476 0.6652928704706296 6.473415419935785 chr22 51304566 25588897 0.498764515423442 1.827091627414142 chrMT 16571 1628588 98.27940377768391 64.36568485877078 chrX 155270560 136937132 0.8819259233688601 3.710352270356625 chrY 59373566 11296708 0.19026494046188838 15.410101434378593