BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525221.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,180,047 number of mapped reads = 1,088,937 (92.28%) number of supplementary alignments = 3,289 (0.28%) number of secondary alignments = 0 number of mapped bases = 63,333,431 bp number of sequenced bases = 63,314,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,648 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6922 >>>>>>> ACTG content number of A's = 15,599,241 bp (24.64%) number of C's = 11,119,828 bp (17.56%) number of T's = 20,958,892 bp (33.1%) number of G's = 15,634,662 bp (24.69%) number of N's = 1,528 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 316,619 number of insertions = 4,679 mapped reads with insertion percentage = 0.43% number of deletions = 12,009 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.2077X There is a 1.89% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 7107861 0.028516923935768247 0.3143459628380234 chr2 243199373 5185780 0.021323163526412545 0.26993099987260943 chr3 198022430 4667957 0.02357287000265576 0.1662444737905186 chr4 191154276 3429547 0.01794125180856535 0.14656163500463656 chr5 180915260 2792624 0.015436088696995488 0.1317347037029514 chr6 171115067 3932276 0.022980302488500325 0.17327191933931962 chr7 159138663 4529498 0.028462586744240775 0.3728283976572782 chr8 146364022 4049254 0.02766563766606523 0.20798604398457737 chr9 141213431 2075595 0.01469828319658914 0.15464307977011685 chr10 135534747 3313813 0.024449914677599244 0.23408578818306516 chr11 135006516 2825390 0.020927804699441322 0.17862491753718565 chr12 133851895 2788302 0.020831247850469355 0.15381020725010897 chr13 115169878 1918073 0.016654293929181725 0.13858999967436406 chr14 107349540 2309079 0.021509910522206244 0.15899512074483657 chr15 102531392 1671393 0.016301280684846257 0.13530738420870667 chr16 90354753 1959547 0.02168725977259879 0.1668089866497502 chr17 81195210 1425751 0.01755954569241215 0.14288224885647566 chr18 78077248 1300134 0.01665189326345109 0.2696960877729695 chr19 59128983 876030 0.014815576990390652 0.22962270711378927 chr20 63025520 1132496 0.017968848174517243 0.1435185485600192 chr21 48129895 789852 0.01641083987405333 0.14131592198309306 chr22 51304566 534178 0.010411899790751567 0.10774963761155326 chrMT 16571 49418 2.9821978154607445 2.229900472698515 chrX 155270560 2495527 0.016072119531223433 0.14323093607593465 chrY 59373566 174056 0.0029315402750105996 0.08458180925305796