BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716238.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 = 1,399,838 number of mapped reads = 1,314,323 (93.89%) number of supplementary alignments = 24,765 (1.77%) number of secondary alignments = 0 number of mapped bases = 104,150,379 bp number of sequenced bases = 104,104,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,631 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6389 >>>>>>> ACTG content number of A's = 27,364,914 bp (26.29%) number of C's = 19,926,998 bp (19.14%) number of T's = 31,372,571 bp (30.14%) number of G's = 25,432,128 bp (24.43%) number of N's = 8,079 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 634,981 number of insertions = 7,670 mapped reads with insertion percentage = 0.57% number of deletions = 23,767 mapped reads with deletion percentage = 1.78% homopolymer indels = 42.94% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.3164X There is a 2.96% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10111035 0.0405657364440428 0.6316453555793152 chr2 243199373 8627536 0.035475157248863465 0.331119718317836 chr3 198022430 6614551 0.03340303924156471 0.19909427960026416 chr4 191154276 6580974 0.03442755316653236 0.2350659043154783 chr5 180915260 6020917 0.03328031587827362 0.20069893952737067 chr6 171115067 5764189 0.033686040049296186 0.21745690898825698 chr7 159138663 5412312 0.03401003815144532 0.37638808074688923 chr8 146364022 5228960 0.03572571953509176 0.3525841367166773 chr9 141213431 4192306 0.029687728499422975 0.26527869677453075 chr10 135534747 4654266 0.03434002057051835 0.29670615637342945 chr11 135006516 5786143 0.04285824989365698 0.35423165275494745 chr12 133851895 4616834 0.034492107862948075 0.2043830168991096 chr13 115169878 3602545 0.03128027104448265 0.19547896022690647 chr14 107349540 3077203 0.028665264890748485 0.198603046017092 chr15 102531392 2925473 0.028532461550897503 0.18541020731508168 chr16 90354753 2329701 0.02578393413349268 0.19101884228466393 chr17 81195210 3217626 0.03962827363830945 0.2561803704600992 chr18 78077248 2641815 0.03383591337645507 0.44170585444395816 chr19 59128983 1996892 0.033771796819167345 0.4520842412080226 chr20 63025520 2170974 0.034445951417774893 0.21226465723903773 chr21 48129895 1362003 0.028298482679008547 0.20863532468379092 chr22 51304566 1154516 0.022503182270365567 0.16438125115749805 chrMT 16571 9058 0.5466175849375415 0.8468192378393125 chrX 155270560 5753597 0.03705529882805858 0.23961924907398205 chrY 59373566 298953 0.005035119500822975 0.15602732668928485