BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472712.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 = 174,910 number of mapped reads = 173,009 (98.91%) number of supplementary alignments = 617 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 86,896 number of mapped paired reads (second in pair) = 86,113 number of mapped paired reads (both in pair) = 171,876 number of mapped paired reads (singletons) = 1,133 number of mapped bases = 17,082,418 bp number of sequenced bases = 17,080,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,598 duplication rate = 20.64% >>>>>>> Insert size mean insert size = 22,218.4899 std insert size = 1,487,026.5654 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 54.9635 >>>>>>> ACTG content number of A's = 4,718,018 bp (27.62%) number of C's = 3,853,458 bp (22.56%) number of T's = 4,689,814 bp (27.46%) number of G's = 3,815,567 bp (22.34%) number of N's = 3,162 bp (0.02%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 105,866 number of insertions = 983 mapped reads with insertion percentage = 0.56% number of deletions = 949 mapped reads with deletion percentage = 0.54% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0055X std coverageData = 0.1956X There is a 0.2% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1816312 0.007287091172382676 0.23422134663733135 chr2 243199373 1343279 0.0055233653912421885 0.23941021335197213 chr3 198022430 1733862 0.008755886896247057 0.22688885274463558 chr4 191154276 594271 0.003108855383386768 0.13011282200314672 chr5 180915260 1105899 0.006112801098149487 0.21204646303174757 chr6 171115067 982784 0.005743410076214972 0.1735508594518301 chr7 159138663 682185 0.004286733262299684 0.1517934660393485 chr8 146364022 754413 0.005154360953540891 0.16849088535157486 chr9 141213431 1098694 0.007780378907442593 0.20959773612677862 chr10 135534747 470533 0.003471678004460362 0.14856793822726086 chr11 135006516 765996 0.005673770590450612 0.23684547158458358 chr12 133851895 1219533 0.009111062641287223 0.3099260717651358 chr13 115169878 289780 0.0025161092903128717 0.1090846739514919 chr14 107349540 322905 0.0030079774911005676 0.10835160350287083 chr15 102531392 428372 0.0041779594682572925 0.16583222858671476 chr16 90354753 522683 0.00578478699399466 0.18358478501088807 chr17 81195210 656244 0.008082299436136689 0.19144901153268434 chr18 78077248 241468 0.003092680725632133 0.11245584092412218 chr19 59128983 334898 0.005663855236610445 0.1571635469876056 chr20 63025520 428751 0.00680281574828736 0.27398188583896527 chr21 48129895 68706 0.0014275119444993596 0.07397214650167744 chr22 51304566 164268 0.0032018202824286635 0.11339741412661941 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 1019606 0.0065666408364856805 0.21178975220092477 chrY 59373566 36876 6.210844738549138E-4 0.05110399747673362