BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472749.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 = 12,700,538 number of mapped reads = 12,569,921 (98.97%) number of supplementary alignments = 45,210 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,312,678 number of mapped paired reads (second in pair) = 6,257,243 number of mapped paired reads (both in pair) = 12,487,570 number of mapped paired reads (singletons) = 82,351 number of mapped bases = 1,238,456,511 bp number of sequenced bases = 1,238,285,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,374,601 duplication rate = 45.62% >>>>>>> Insert size mean insert size = 23,845.5219 std insert size = 1,523,470.4937 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 55.2062 >>>>>>> ACTG content number of A's = 348,218,983 bp (28.12%) number of C's = 272,386,617 bp (22%) number of T's = 346,361,371 bp (27.97%) number of G's = 271,083,121 bp (21.89%) number of N's = 235,848 bp (0.02%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 8,110,764 number of insertions = 73,927 mapped reads with insertion percentage = 0.58% number of deletions = 71,782 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.4001X std coverageData = 13.2339X There is a 3.66% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 84966247 0.34088680164211105 9.664322578347978 chr2 243199373 87540668 0.3599543326125269 11.691945870502149 chr3 198022430 169633139 0.8566359831055502 19.01739559642962 chr4 191154276 51327165 0.2685117281917356 9.861060766049869 chr5 180915260 71453869 0.3949576669209662 13.57838423895448 chr6 171115067 79555635 0.4649247807032679 12.423310430663573 chr7 159138663 64442868 0.40494790382900225 17.588604965991205 chr8 146364022 48807544 0.33346681331290556 11.486544043649895 chr9 141213431 69587133 0.4927798475486372 16.379441731276007 chr10 135534747 37034836 0.2732497519621297 11.038987648175665 chr11 135006516 46752574 0.3462986482815392 9.730793809298945 chr12 133851895 54895313 0.41011980443011287 11.565690091892728 chr13 115169878 44260468 0.3843059380509199 19.36464729384832 chr14 107349540 33867010 0.31548351301738226 10.08728234358817 chr15 102531392 27893704 0.27205037848310887 8.497377991385086 chr16 90354753 33493126 0.3706847164974265 9.281329085755713 chr17 81195210 59568073 0.7336402356740009 16.106287045654415 chr18 78077248 20597812 0.26381324300774533 9.208215513584257 chr19 59128983 37435985 0.6331241144465481 16.124298329149692 chr20 63025520 22099334 0.3506410419144499 11.57602958248744 chr21 48129895 5513430 0.11455312753123605 4.888239094404729 chr22 51304566 10294274 0.20065025011613977 5.514567817578589 chrMT 16571 1366 0.08243316637499246 0.3358739564626605 chrX 155270560 76128192 0.49029379426466935 19.395931329195495 chrY 59373566 1306746 0.022008885233539787 0.7823877587734953