BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971312.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 = 10,363,302 number of mapped reads = 9,517,305 (91.84%) number of supplementary alignments = 1,258 (0.01%) number of secondary alignments = 0 number of mapped bases = 458,079,455 bp number of sequenced bases = 457,982,964 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 821,658 duplication rate = 7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.9881 >>>>>>> ACTG content number of A's = 129,836,274 bp (28.35%) number of C's = 96,337,314 bp (21.04%) number of T's = 132,408,406 bp (28.91%) number of G's = 99,375,450 bp (21.7%) number of N's = 25,520 bp (0.01%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 2,201,868 number of insertions = 28,444 mapped reads with insertion percentage = 0.3% number of deletions = 66,247 mapped reads with deletion percentage = 0.69% homopolymer indels = 41.68% >>>>>>> Coverage mean coverageData = 0.148X std coverageData = 1.1987X There is a 10.27% of reference with a coverageData >= 1X There is a 2.83% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 35944608 0.14421070589830146 2.128839886185021 chr2 243199373 37065682 0.15240862483638065 1.122685032427646 chr3 198022430 31454019 0.1588406878958106 0.5518336044397395 chr4 191154276 32311848 0.16903544443860624 0.764547939669472 chr5 180915260 28213974 0.1559513221825511 0.5413458035018958 chr6 171115067 26570437 0.1552781848251855 0.6056460744297419 chr7 159138663 27595306 0.17340415886238783 1.9981779472475105 chr8 146364022 23322244 0.15934410438652744 1.966410644835041 chr9 141213431 18430715 0.13051672825653532 1.0471421572288002 chr10 135534747 24147390 0.17816383277714018 1.3893427368468674 chr11 135006516 22305635 0.1652189513578737 0.983275257149184 chr12 133851895 21050168 0.157264624456755 0.5749006552576428 chr13 115169878 15293531 0.13279106712260302 0.48372706428057577 chr14 107349540 13609508 0.12677751576765023 0.6803970717677368 chr15 102531392 13989747 0.13644354891816937 0.499292500263698 chr16 90354753 12468944 0.13799986814196702 0.661470929461507 chr17 81195210 11312797 0.1393283791001957 0.6790643483294033 chr18 78077248 14698282 0.18825307469853444 2.326127332792598 chr19 59128983 9149557 0.15473895432972354 1.7565421913991406 chr20 63025520 8642471 0.13712653223646548 0.5616964272811914 chr21 48129895 6135120 0.1274700474621854 0.7332582169601781 chr22 51304566 4897370 0.09545680593029478 0.530377173812388 chrMT 16571 82843 4.999275843340776 4.2041254899248095 chrX 155270560 14881681 0.09584354561482872 0.5776607753418042 chrY 59373566 4505578 0.0758852516960157 0.7504113998586347