BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717068.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 = 1,075,835 number of mapped reads = 896,735 (83.35%) number of supplementary alignments = 1,264 (0.12%) number of secondary alignments = 0 number of mapped bases = 49,359,234 bp number of sequenced bases = 49,346,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,830 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7114 >>>>>>> ACTG content number of A's = 11,562,908 bp (23.43%) number of C's = 10,080,154 bp (20.43%) number of T's = 15,105,369 bp (30.61%) number of G's = 12,596,725 bp (25.53%) number of N's = 928 bp (0%) GC percentage = 45.95% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 324,207 number of insertions = 2,865 mapped reads with insertion percentage = 0.32% number of deletions = 7,638 mapped reads with deletion percentage = 0.84% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.1578X There is a 1.43% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4873374 0.019552103743805716 0.19995450962392716 chr2 243199373 4049440 0.0166507008223249 0.20158987656254798 chr3 198022430 3424910 0.017295565961896336 0.14563309927183204 chr4 191154276 3220249 0.016846335156007707 0.15129680567246026 chr5 180915260 3139823 0.0173552137061296 0.14468067368027746 chr6 171115067 2167771 0.012668498677559469 0.13313019025790584 chr7 159138663 2844486 0.017874261014747875 0.1789279032902586 chr8 146364022 3138846 0.021445475172853612 0.16834740955792613 chr9 141213431 2217440 0.01570275563944056 0.14881343017205031 chr10 135534747 2436785 0.017979042673094008 0.17912561880106517 chr11 135006516 2102700 0.015574803811691578 0.156502852190145 chr12 133851895 2371062 0.017714071212813237 0.14553819439415683 chr13 115169878 868051 0.007537135708349018 0.09484790198879313 chr14 107349540 1550900 0.014447197444907542 0.13260485107796605 chr15 102531392 979970 0.009557755735921346 0.10679558380363838 chr16 90354753 1281747 0.01418571749070024 0.14016925969892313 chr17 81195210 1839574 0.0226561887086689 0.17238798672121483 chr18 78077248 1384244 0.01772915971628508 0.18602705344751408 chr19 59128983 1223194 0.020686877026110866 0.19043642660672205 chr20 63025520 1257075 0.019945491921367724 0.1594763405722451 chr21 48129895 698260 0.01450782304844006 0.14169571108860074 chr22 51304566 524110 0.010215659947303715 0.1120778898554656 chrMT 16571 21344 1.2880333112063242 1.3788714241354776 chrX 155270560 1595989 0.010278761150858217 0.11671217678310969 chrY 59373566 147890 0.002490839105065712 0.07975364480927959