BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174061.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 = 3,990,448 number of mapped reads = 3,887,135 (97.41%) number of supplementary alignments = 374,347 (9.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,946,851 number of mapped paired reads (second in pair) = 1,940,284 number of mapped paired reads (both in pair) = 3,819,390 number of mapped paired reads (singletons) = 67,745 number of mapped bases = 457,468,538 bp number of sequenced bases = 457,225,713 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,029,035 duplication rate = 65.61% >>>>>>> Insert size mean insert size = 777,014.0043 std insert size = 8,131,290.5918 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.7549 >>>>>>> ACTG content number of A's = 138,127,675 bp (30.21%) number of C's = 89,194,660 bp (19.51%) number of T's = 137,662,964 bp (30.11%) number of G's = 92,234,669 bp (20.17%) number of N's = 5,745 bp (0%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 4,559,834 number of insertions = 45,991 mapped reads with insertion percentage = 1.14% number of deletions = 97,463 mapped reads with deletion percentage = 2.45% homopolymer indels = 43.6% >>>>>>> Coverage mean coverageData = 0.1478X std coverageData = 2.2565X There is a 3.03% of reference with a coverageData >= 1X There is a 2.42% of reference with a coverageData >= 2X There is a 1.88% of reference with a coverageData >= 3X There is a 1.56% of reference with a coverageData >= 4X There is a 1.19% of reference with a coverageData >= 5X There is a 0.97% of reference with a coverageData >= 6X There is a 0.72% of reference with a coverageData >= 7X There is a 0.59% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 33876959 0.13591524411889028 1.6426431483516408 chr2 243199373 49123410 0.20198822634300131 6.610769065495686 chr3 198022430 39511551 0.19953068447852093 1.3183334353362677 chr4 191154276 21379981 0.1118467315897239 1.0711752054704369 chr5 180915260 29215282 0.16148600178890382 1.16350864714428 chr6 171115067 26175376 0.15296944014871583 1.2523295234600824 chr7 159138663 23746667 0.14921997302440576 1.4638824908706636 chr8 146364022 26801157 0.18311301256807497 1.6067031813507826 chr9 141213431 16557781 0.11725358475285541 1.2179313283595592 chr10 135534747 23470829 0.17317204273823597 2.1900506241933866 chr11 135006516 14910902 0.11044579507555027 0.974247649363016 chr12 133851895 22269887 0.16637707669360977 1.1897844767814778 chr13 115169878 10143750 0.08807641525851057 0.8674042659516782 chr14 107349540 13248392 0.12341358891710202 1.0180349687690735 chr15 102531392 14962282 0.14592879027722552 1.1020156100770258 chr16 90354753 14372611 0.1590686767745356 1.345144892776502 chr17 81195210 17439373 0.21478327354532367 1.4113347665368072 chr18 78077248 8438248 0.10807563299362191 1.5180831657490204 chr19 59128983 5358314 0.09062077052805051 1.219515595693818 chr20 63025520 19183723 0.304380241527559 1.710629715127322 chr21 48129895 5621012 0.11678837030498404 1.0233553732692056 chr22 51304566 3183935 0.062059486089405765 0.6855336917232908 chrMT 16571 1321019 79.71872548427977 57.54597027529061 chrX 155270560 16411943 0.10569900050595554 0.9367113645056101 chrY 59373566 744154 0.012533422701947867 0.4468292086568531