BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714235.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 281,986 number of mapped reads = 21,963 (7.79%) number of supplementary alignments = 654 (0.23%) number of secondary alignments = 0 number of mapped bases = 2,203,588 bp number of sequenced bases = 2,173,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,161 duplication rate = 36.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 33.6416 >>>>>>> ACTG content number of A's = 429,365 bp (19.75%) number of C's = 297,497 bp (13.69%) number of T's = 386,517 bp (17.78%) number of G's = 1,059,961 bp (48.77%) number of N's = 123 bp (0.01%) GC percentage = 62.46% >>>>>>> Mismatches and indels general error rate = 0.0358 number of mismatches = 67,966 number of insertions = 2,149 mapped reads with insertion percentage = 8.2% number of deletions = 4,916 mapped reads with deletion percentage = 20.72% homopolymer indels = 34.39% >>>>>>> Coverage mean coverageData = 0.0007X std coverageData = 0.8824X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 74289 2.980494078688775E-4 0.10470363830425572 chr2 243199373 874147 0.003594363707508407 3.1051503018503563 chr3 198022430 72283 3.650243055799285E-4 0.13386102819142637 chr4 191154276 77315 4.04463879217643E-4 0.17576527747035026 chr5 180915260 89513 4.947786051878653E-4 0.23565769831568945 chr6 171115067 81482 4.7618249771073636E-4 0.1494340510534593 chr7 159138663 79678 5.006828541722761E-4 0.1982666967346093 chr8 146364022 70278 4.801589833326663E-4 0.15452815126200536 chr9 141213431 26998 1.9118578033841554E-4 0.06919946745418712 chr10 135534747 21718 1.6023935175826166E-4 0.055201594400821195 chr11 135006516 39334 2.9134890052269773E-4 0.07873990610694315 chr12 133851895 46095 3.443731596030075E-4 0.08845276611002531 chr13 115169878 23576 2.0470630350064275E-4 0.09615976217828202 chr14 107349540 55766 5.194805678720188E-4 0.14671879185710857 chr15 102531392 23187 2.2614537409186837E-4 0.07662623018829945 chr16 90354753 22310 2.46915621583294E-4 0.07063841629481415 chr17 81195210 12739 1.5689349162345908E-4 0.04978783688940643 chr18 78077248 47523 6.08666432505408E-4 0.15790233965825742 chr19 59128983 8347 1.4116596593585925E-4 0.039227575868476874 chr20 63025520 17365 2.755233118267013E-4 0.07005192106918397 chr21 48129895 9766 2.0290923136233728E-4 0.07258982437366564 chr22 51304566 3664 7.141664545023147E-5 0.01935612313294902 chrMT 16571 8502 0.5130649930601654 4.758110016829914 chrX 155270560 406215 0.0026161752749523154 0.3487521366690468 chrY 59373566 11498 1.9365520339472282E-4 0.030277344930661646