BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472588.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 = 8,652,308 number of mapped reads = 7,988,281 (92.33%) number of supplementary alignments = 200,409 (2.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,037,039 number of mapped paired reads (second in pair) = 3,951,242 number of mapped paired reads (both in pair) = 7,792,958 number of mapped paired reads (singletons) = 195,323 number of mapped bases = 656,358,029 bp number of sequenced bases = 656,087,626 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,241,487 duplication rate = 12.7% >>>>>>> Insert size mean insert size = 179,530.5541 std insert size = 4,157,132.1776 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 51.2149 >>>>>>> ACTG content number of A's = 168,678,965 bp (25.71%) number of C's = 126,605,879 bp (19.3%) number of T's = 201,008,743 bp (30.64%) number of G's = 159,359,875 bp (24.29%) number of N's = 434,164 bp (0.07%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0123 number of mismatches = 7,978,711 number of insertions = 57,741 mapped reads with insertion percentage = 0.71% number of deletions = 143,650 mapped reads with deletion percentage = 1.76% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.212X std coverageData = 2.1808X There is a 11.61% of reference with a coverageData >= 1X There is a 5.06% of reference with a coverageData >= 2X There is a 1.95% of reference with a coverageData >= 3X There is a 0.94% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 55328275 0.22197848405761847 4.398109472530473 chr2 243199373 60709850 0.24962996101145377 1.911330224551601 chr3 198022430 46489102 0.2347668493917583 0.7584056017152835 chr4 191154276 41533652 0.2172781737825211 1.195014366021099 chr5 180915260 40274884 0.2226173955696164 0.7744099754559768 chr6 171115067 39591013 0.23137070097982662 1.1666484783572117 chr7 159138663 35845934 0.22524968680929536 3.002231782339971 chr8 146364022 34523504 0.2358742505723162 1.6672950298711688 chr9 141213431 27612082 0.1955343893598903 2.51236836835545 chr10 135534747 32032326 0.23634032385805834 2.4799147293939727 chr11 135006516 30106023 0.22299681446486627 1.803878415137826 chr12 133851895 30185750 0.2255160451781426 0.7638224316446461 chr13 115169878 19548452 0.1697358053986998 0.6429177513438221 chr14 107349540 22033092 0.20524626374738075 4.094005468932449 chr15 102531392 20178117 0.19679940559082626 0.7101635051583476 chr16 90354753 20153966 0.22305374461042465 1.145403748027078 chr17 81195210 18218403 0.22437780504539614 1.3598383670836294 chr18 78077248 17663073 0.22622560928376984 4.124203203699036 chr19 59128983 10704264 0.1810324388633574 2.4843573513419535 chr20 63025520 13917768 0.22082749971757473 0.9600725247228691 chr21 48129895 7867750 0.16346908714427905 0.8540120827298245 chr22 51304566 8317571 0.16212145718180326 0.987639063026484 chrMT 16571 22422 1.3530867177599422 1.8626861902135536 chrX 155270560 18625594 0.11995573404256415 0.8719250618326395 chrY 59373566 4875162 0.08210997466448285 1.1290757985851936