BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819108.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,285,587 number of mapped reads = 1,180,801 (91.85%) number of supplementary alignments = 4,705 (0.37%) number of secondary alignments = 0 number of mapped bases = 68,786,078 bp number of sequenced bases = 68,765,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,597 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8816 >>>>>>> ACTG content number of A's = 16,889,292 bp (24.56%) number of C's = 13,513,562 bp (19.65%) number of T's = 21,466,636 bp (31.22%) number of G's = 16,894,605 bp (24.57%) number of N's = 1,084 bp (0%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 347,515 number of insertions = 4,200 mapped reads with insertion percentage = 0.35% number of deletions = 12,701 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0222X std coverageData = 0.2205X There is a 2.02% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 7045207 0.028265554451717894 0.3960154360764241 chr2 243199373 5070471 0.020849029902721007 0.23839683899050865 chr3 198022430 3380201 0.017069788508301813 0.14113559780074486 chr4 191154276 3271611 0.017115029119202124 0.15772227024843521 chr5 180915260 4235389 0.02341089966650685 0.16498725185273064 chr6 171115067 2990703 0.01747773035088722 0.17383130979155492 chr7 159138663 3478011 0.021855223202421902 0.26121512904844224 chr8 146364022 6013691 0.0410872215577678 0.2545084846201638 chr9 141213431 3347612 0.023706045354850134 0.2002024899175694 chr10 135534747 3740627 0.027599025953101163 0.23021302157829907 chr11 135006516 2409276 0.017845627539932962 0.19877104882875293 chr12 133851895 3230735 0.024136639978089215 0.1676829794356755 chr13 115169878 1541982 0.013388761252312866 0.12461511375039927 chr14 107349540 1641250 0.015288840548361922 0.13611386358724667 chr15 102531392 1843313 0.017978035448889644 0.14653660815829897 chr16 90354753 2169127 0.02400678357230416 0.17746936216295514 chr17 81195210 2492042 0.0306919829384024 0.20057949363502742 chr18 78077248 1556159 0.019931017548159485 0.3367661211733293 chr19 59128983 1423597 0.02407612862206678 0.28109059409117887 chr20 63025520 2004038 0.03179724657567284 0.19326625213273577 chr21 48129895 974234 0.02024176450000566 0.1634878697038573 chr22 51304566 574722 0.011202160836912644 0.11332605674320406 chrMT 16571 16377 0.9882928006758795 1.2179071630893044 chrX 155270560 4100704 0.026410054810132713 0.19088326281114845 chrY 59373566 234999 0.003957973486045962 0.1171311822956721