BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068933.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 = 2,321,685 number of mapped reads = 1,900,995 (81.88%) number of supplementary alignments = 9,010 (0.39%) number of secondary alignments = 0 number of mapped bases = 124,454,355 bp number of sequenced bases = 124,403,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,813 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4557 >>>>>>> ACTG content number of A's = 33,727,662 bp (27.11%) number of C's = 21,488,414 bp (17.27%) number of T's = 41,170,332 bp (33.09%) number of G's = 27,715,675 bp (22.28%) number of N's = 301,546 bp (0.24%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,169,514 number of insertions = 10,782 mapped reads with insertion percentage = 0.56% number of deletions = 30,798 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.4216X There is a 3.43% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% 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% 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 22766909 0.09134143340810373 0.6486479544492886 chr2 243199373 9969046 0.040991248772668507 0.3057533330032424 chr3 198022430 15464568 0.07809503196178331 0.42293953204680157 chr4 191154276 6923729 0.036220633641488614 0.21840369836784404 chr5 180915260 2380876 0.013160172337037793 0.12882173109260978 chr6 171115067 13519678 0.07900927859263264 0.43436681004721467 chr7 159138663 9441224 0.05932702852982999 0.40703911017394273 chr8 146364022 8991086 0.061429618270533726 0.3812045428884153 chr9 141213431 3157590 0.02236040847984212 0.2507098172559843 chr10 135534747 9170046 0.06765826625994292 1.3075989754365807 chr11 135006516 2109508 0.015625231007368564 0.23209045207375334 chr12 133851895 4192190 0.03131961635657082 0.2000929232724975 chr13 115169878 851290 0.007391602863380649 0.09532042283794707 chr14 107349540 3745274 0.034888589182589885 0.2087025287705726 chr15 102531392 1973150 0.019244350062076598 0.1547704138746358 chr16 90354753 783319 0.008669372379336812 0.20011283560000692 chr17 81195210 1911878 0.02354668458890617 0.17876054654753962 chr18 78077248 2356198 0.030177779831584227 0.3942643815521359 chr19 59128983 1211640 0.020491473699116386 0.3418298121480265 chr20 63025520 319050 0.005062235107302565 0.08539271816042292 chr21 48129895 415148 0.008625574603892239 0.11579410322555854 chr22 51304566 1177596 0.02295304476408591 0.17019391205362294 chrMT 16571 40246 2.4287007422605758 2.0338895854065706 chrX 155270560 1403272 0.009037592187469409 0.13383170736676375 chrY 59373566 179844 0.0030290247346773814 0.09551475367980422