BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472549.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 = 15,109,412 number of mapped reads = 14,944,439 (98.91%) number of supplementary alignments = 56,316 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,500,450 number of mapped paired reads (second in pair) = 7,443,989 number of mapped paired reads (both in pair) = 14,849,974 number of mapped paired reads (singletons) = 94,465 number of mapped bases = 1,474,529,921 bp number of sequenced bases = 1,474,335,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,503,081 duplication rate = 45% >>>>>>> Insert size mean insert size = 27,576.4966 std insert size = 1,597,172.0708 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 54.826 >>>>>>> ACTG content number of A's = 418,128,321 bp (28.36%) number of C's = 321,189,030 bp (21.79%) number of T's = 416,562,383 bp (28.25%) number of G's = 318,228,509 bp (21.58%) number of N's = 227,134 bp (0.02%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,261,149 number of insertions = 88,774 mapped reads with insertion percentage = 0.59% number of deletions = 80,514 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.24% >>>>>>> Coverage mean coverageData = 0.4763X std coverageData = 18.9832X There is a 4.98% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 140695137 0.5644725635407745 22.189378627233854 chr2 243199373 134147004 0.5515927214170901 22.37859609944654 chr3 198022430 135811527 0.6858391092362618 19.180024984533745 chr4 191154276 80146870 0.41927845757423704 17.707255011512256 chr5 180915260 80180320 0.4431926859016757 14.896239861830848 chr6 171115067 118173358 0.6906075547397589 22.34149734050885 chr7 159138663 90688342 0.5698699504594933 18.855995413388165 chr8 146364022 61598037 0.4208550445545969 12.607145836411515 chr9 141213431 98680427 0.6988034091459756 19.522575837510633 chr10 135534747 20708906 0.15279407279964893 5.297295247467373 chr11 135006516 57484683 0.4257919151102307 16.67124492621424 chr12 133851895 75786219 0.5661945914176262 36.04923862567641 chr13 115169878 40188500 0.348949748822344 12.534025801389852 chr14 107349540 27477619 0.25596401251463213 9.029706336103425 chr15 102531392 25054995 0.24436413581510724 9.636841052031144 chr16 90354753 58064801 0.642631395384369 26.114652393410573 chr17 81195210 38209368 0.47058647917777413 19.16767108478563 chr18 78077248 16674275 0.2135612541056775 7.59646989123636 chr19 59128983 18869050 0.3191167688441386 10.125415624415883 chr20 63025520 40632999 0.6447070805603825 24.578900538868403 chr21 48129895 6549246 0.13607438786226314 5.395076125127361 chr22 51304566 5165544 0.10068390404082163 4.2723995393342244 chrMT 16571 2849 0.17192686017741837 0.4452513564984771 chrX 155270560 100051698 0.6443700467107223 23.33595287232377 chrY 59373566 3488147 0.0587491578322919 2.336540812542225