BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549019.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,289,140 number of mapped reads = 6,312,534 (86.6%) number of secondary alignments = 0 number of mapped bases = 250,049,105 bp number of sequenced bases = 250,021,524 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 239,666 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.98 >>>>>>> ACTG content number of A's = 74,361,275 bp (29.74%) number of C's = 50,629,605 bp (20.25%) number of T's = 74,286,704 bp (29.71%) number of G's = 50,741,333 bp (20.29%) number of N's = 2,607 bp (0%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 659,807 number of insertions = 7,536 mapped reads with insertion percentage = 0.12% number of deletions = 20,773 mapped reads with deletion percentage = 0.33% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0808X std coverageData = 1.1182X There is a 6.28% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 19410322 0.07787471871534475 0.7942052014389794 chr2 243199373 21189917 0.08712981755919247 0.4711373016487204 chr3 198022430 17210201 0.08691036161913578 0.36274704603439883 chr4 191154276 16723680 0.08748786765303644 0.3729654386192684 chr5 180915260 15580930 0.08612280688760031 0.3651680972639019 chr6 171115067 14760984 0.08626349659787703 0.3930985596670764 chr7 159138663 13803837 0.08674093862407277 0.6454058205833479 chr8 146364022 13183244 0.09007161609702144 4.674610639847089 chr9 141213431 10459787 0.07407076597409491 0.43613438717820324 chr10 135534747 11498925 0.08484115885057873 0.432929361920731 chr11 135006516 11211740 0.08304591757630424 0.5420979652309426 chr12 133851895 11475172 0.08573036638741648 0.36875206829304424 chr13 115169878 8290828 0.07198781611976701 0.3278693838251611 chr14 107349540 7616561 0.07095103528156711 0.3715799528777449 chr15 102531392 7165252 0.06988349480323061 0.3218823944760686 chr16 90354753 6692179 0.07406560006865383 0.3489844916239672 chr17 81195210 6223289 0.07664601150732907 0.361977598453698 chr18 78077248 6672338 0.0854581606154971 0.7364565582969878 chr19 59128983 4581715 0.0774867885009962 0.7008270392347978 chr20 63025520 4920026 0.07806402866648304 0.352129946581009 chr21 48129895 3255920 0.06764859969048342 0.3470089661529983 chr22 51304566 2667682 0.051996970406103814 0.3063766639403144 chrMT 16571 33142 2.0 2.5942379623454506 chrX 155270560 14702619 0.09469031991640914 0.4389174401754144 chrY 59373566 718815 0.012106650289457095 0.178146984088074