BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173844.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,556,928 number of mapped reads = 1,517,124 (97.44%) number of supplementary alignments = 142,213 (9.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 758,967 number of mapped paired reads (second in pair) = 758,157 number of mapped paired reads (both in pair) = 1,491,578 number of mapped paired reads (singletons) = 25,546 number of mapped bases = 180,060,133 bp number of sequenced bases = 179,961,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,170,428 duplication rate = 64.13% >>>>>>> Insert size mean insert size = 1,060,268.0693 std insert size = 9,483,433.7772 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.0745 >>>>>>> ACTG content number of A's = 54,066,360 bp (30.04%) number of C's = 35,416,493 bp (19.68%) number of T's = 53,821,221 bp (29.91%) number of G's = 36,655,291 bp (20.37%) number of N's = 2,155 bp (0%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,884,460 number of insertions = 20,695 mapped reads with insertion percentage = 1.31% number of deletions = 40,268 mapped reads with deletion percentage = 2.59% homopolymer indels = 42.1% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 1.0152X There is a 1.23% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 14125951 0.056673684275394445 0.824736101025196 chr2 243199373 16554094 0.06806799621148694 2.5329181366927127 chr3 198022430 12275440 0.061990149297733596 0.7238051884117058 chr4 191154276 12284201 0.0642632812461909 0.8561777224439991 chr5 180915260 11130328 0.0615223281883463 0.721130869228079 chr6 171115067 10812964 0.0631911858468898 0.7542193025171988 chr7 159138663 10262700 0.06448904248994476 0.8223824940482084 chr8 146364022 9256304 0.06324166194339753 0.8456697987783368 chr9 141213431 7461173 0.05283614276038658 0.7753843841998828 chr10 135534747 8741320 0.06449504790088995 0.9231177869064697 chr11 135006516 8366172 0.06196865342410584 0.7236182732902501 chr12 133851895 8447996 0.06311450428101896 0.7254022100637624 chr13 115169878 5955702 0.05171232359905773 0.6661197648745958 chr14 107349540 5656713 0.05269433851323443 0.6573351325088687 chr15 102531392 5198432 0.05070088193087245 0.6462145367959191 chr16 90354753 5312841 0.05879979551269428 0.728590170010433 chr17 81195210 4996935 0.06154223876014361 0.7340495797515723 chr18 78077248 4861767 0.0622686778099556 0.9842609095432567 chr19 59128983 3301271 0.05583168917348029 0.7032560791514604 chr20 63025520 3969262 0.06297864737966462 0.7178714451029474 chr21 48129895 2541808 0.05281141793473682 0.6967829398499534 chr22 51304566 2270139 0.04424828386619624 0.5975706544790402 chrMT 16571 266457 16.0797175789029 14.901073790266913 chrX 155270560 4757123 0.030637636651790267 0.5039535000540858 chrY 59373566 1253040 0.021104341282111975 0.4703285942800643