BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231874.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,720,455 number of mapped reads = 2,874,031 (60.88%) number of supplementary alignments = 21,992 (0.47%) number of secondary alignments = 0 number of mapped bases = 184,484,485 bp number of sequenced bases = 184,416,639 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,209 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1344 >>>>>>> ACTG content number of A's = 53,118,228 bp (28.8%) number of C's = 37,374,985 bp (20.27%) number of T's = 52,105,903 bp (28.25%) number of G's = 41,803,799 bp (22.67%) number of N's = 13,724 bp (0.01%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,217,183 number of insertions = 13,952 mapped reads with insertion percentage = 0.48% number of deletions = 41,612 mapped reads with deletion percentage = 1.43% homopolymer indels = 43.85% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 4.6431X There is a 5.02% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 19808516 0.07947228344117145 1.6581620504868269 chr2 243199373 13772061 0.05662868629188448 16.377083169738174 chr3 198022430 12081783 0.06101219442666166 0.2800709774898927 chr4 191154276 8813798 0.04610829631663589 0.2681674175896198 chr5 180915260 11169239 0.06173740678370636 0.29190713246789624 chr6 171115067 14337516 0.08378874082432496 0.47938399403651294 chr7 159138663 12384579 0.07782256534353314 1.2321313181493998 chr8 146364022 9701968 0.06628656323751475 0.9797240473331729 chr9 141213431 5940347 0.04206644479872456 0.5074177774572474 chr10 135534747 8179337 0.060348635173237165 0.5300906333131152 chr11 135006516 7172094 0.053124058101017876 0.5409311565875208 chr12 133851895 6371095 0.04759809340017188 0.26161586815706467 chr13 115169878 4962915 0.04309212691881118 0.23270480561019685 chr14 107349540 7748029 0.07217570750652495 0.37650433938858524 chr15 102531392 5096496 0.0497066888548631 0.25782205985670825 chr16 90354753 5154553 0.05704794522541609 0.3237056328515885 chr17 81195210 5007473 0.06167202474136097 0.34912746277154255 chr18 78077248 4615893 0.059119565792072996 1.1204629099734862 chr19 59128983 5082629 0.08595833620206185 0.9885120419780807 chr20 63025520 4321216 0.06856295671975415 0.3160750016869515 chr21 48129895 4209052 0.08745192566906701 0.36343663038005053 chr22 51304566 1864827 0.036348168309230024 0.21269108097189168 chrMT 16571 84784 5.1164081829702495 3.782498419013284 chrX 155270560 6118069 0.03940263369952424 0.31179139471681444 chrY 59373566 486216 0.008189098832298534 0.1767009236247092