BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549036.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 = 8,208,192 number of mapped reads = 7,079,038 (86.24%) number of secondary alignments = 0 number of mapped bases = 280,737,263 bp number of sequenced bases = 280,711,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,731 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2903 >>>>>>> ACTG content number of A's = 80,520,893 bp (28.68%) number of C's = 59,687,241 bp (21.26%) number of T's = 80,862,041 bp (28.81%) number of G's = 59,640,928 bp (21.25%) number of N's = 210 bp (0%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 677,220 number of insertions = 7,496 mapped reads with insertion percentage = 0.11% number of deletions = 19,516 mapped reads with deletion percentage = 0.28% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.0907X std coverageData = 0.5082X There is a 6.56% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% 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% 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 24106852 0.09671731971331779 0.6611147549808835 chr2 243199373 20445867 0.0840703935531939 0.4231681661186007 chr3 198022430 19760469 0.09978904409970123 0.42024471634548466 chr4 191154276 18411113 0.09631546510631026 0.41912756304956306 chr5 180915260 19244363 0.10637224853226865 0.43316228502771115 chr6 171115067 15763867 0.09212436564688953 0.4084909051166081 chr7 159138663 14745834 0.09266028582884349 0.4412359591969511 chr8 146364022 15035978 0.10273001380079594 1.1506395695780374 chr9 141213431 12997035 0.09203823537153488 0.44308878854694084 chr10 135534747 13668224 0.10084664119378922 0.4661933202993968 chr11 135006516 13082364 0.09690172287684248 0.42703162544880363 chr12 133851895 13723688 0.10252890330764462 0.43104817977314624 chr13 115169878 8971153 0.07789495965255776 0.3748837493763098 chr14 107349540 8951069 0.08338246256108782 0.4121849798984075 chr15 102531392 7733811 0.07542871357876425 0.36491725772851846 chr16 90354753 8484568 0.09390284094960671 0.4259520747073621 chr17 81195210 8099784 0.09975691915816216 0.4230064636842579 chr18 78077248 6432842 0.08239073692761302 0.5555241898261492 chr19 59128983 6254597 0.1057788698987094 0.6509685313875406 chr20 63025520 6278117 0.0996122999064506 0.4312493327293405 chr21 48129895 3839230 0.07976809423747963 0.414424998581004 chr22 51304566 3832833 0.07470744416783488 0.5451146385771528 chrMT 16571 3486 0.21036750950455615 0.5964238194350918 chrX 155270560 8830734 0.05687320249247507 0.3219443502145109 chrY 59373566 2039385 0.03434836640938831 0.26929981137030373