BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504719.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,026,636 number of mapped reads = 1,788,219 (88.24%) number of secondary alignments = 0 number of mapped bases = 57,217,318 bp number of sequenced bases = 57,217,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,584 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.3341 >>>>>>> ACTG content number of A's = 16,597,982 bp (29.01%) number of C's = 11,534,738 bp (20.16%) number of T's = 17,494,864 bp (30.58%) number of G's = 11,589,654 bp (20.26%) number of N's = 80 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 32,667 >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.9776X There is a 1.27% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 4064562 0.016307128879731056 0.2157195490289518 chr2 243199373 4398550 0.018086189720563136 0.19587045351681495 chr3 198022430 4043418 0.020418989909375417 0.22788882439628086 chr4 191154276 3558788 0.018617360147360762 0.20519041422708817 chr5 180915260 3416154 0.01888261940977229 0.19549142729111707 chr6 171115067 3123626 0.018254535119341653 0.2294414288407598 chr7 159138663 2810846 0.01766287303796187 0.22385894577504414 chr8 146364022 2966218 0.020266032317696216 0.22828972650241344 chr9 141213431 1941032 0.01374537808659291 0.18309635222467455 chr10 135534747 8157638 0.0601885360069326 4.574072001377541 chr11 135006516 2531730 0.018752650427628248 0.2301919662706778 chr12 133851895 2387732 0.017838611847818816 0.1980926573424507 chr13 115169878 1452554 0.012612273497415704 0.15727969371224623 chr14 107349540 1724690 0.016066114489172473 0.20733756405189863 chr15 102531392 1423180 0.013880431858371726 0.16987937485734267 chr16 90354753 1282792 0.014197283013988208 0.2047533258705789 chr17 81195210 944878 0.01163711504656494 0.17794904434382297 chr18 78077248 1481220 0.0189712116902481 0.20863785565376405 chr19 59128983 562308 0.009509854076130482 0.12206255556260827 chr20 63025520 923666 0.014655428467706415 0.16928804772878803 chr21 48129895 610930 0.01269335825478115 0.1627581475314367 chr22 51304566 326102 0.006356198393725814 0.12573100485582459 chrMT 16571 0 0.0 0.0 chrX 155270560 2735282 0.017616230662142265 0.2417693349768922 chrY 59373566 349422 0.005885144240788906 0.12025196967686926