BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238332.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 = 2,354,806 number of mapped reads = 2,083,121 (88.46%) number of supplementary alignments = 27,919 (1.19%) number of secondary alignments = 0 number of mapped bases = 137,951,905 bp number of sequenced bases = 137,887,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,791 duplication rate = 5.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9411 >>>>>>> ACTG content number of A's = 38,511,299 bp (27.93%) number of C's = 26,389,408 bp (19.14%) number of T's = 42,655,954 bp (30.94%) number of G's = 30,310,581 bp (21.98%) number of N's = 19,952 bp (0.01%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,200,179 number of insertions = 11,744 mapped reads with insertion percentage = 0.56% number of deletions = 37,773 mapped reads with deletion percentage = 1.79% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.4805X There is a 3.36% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 14234736 0.057110132536038895 0.6185030387095137 chr2 243199373 7698186 0.03165380693641837 0.6492444780798313 chr3 198022430 9240802 0.04666543077973541 0.2727673134270245 chr4 191154276 10528759 0.05507990310402473 0.3559329395172719 chr5 180915260 8727817 0.04824256947700266 0.28269056587104546 chr6 171115067 4746215 0.027736978883338193 0.24595200983214574 chr7 159138663 7212610 0.04532280128556817 0.5168778538225384 chr8 146364022 9639443 0.06585937492206931 0.965137590837689 chr9 141213431 5549569 0.03929915844902883 0.557822812676625 chr10 135534747 2262476 0.01669295918632585 0.3792102452774306 chr11 135006516 6445328 0.04774086607790101 0.40163809174047155 chr12 133851895 7625343 0.05696850985934865 0.32732671290180293 chr13 115169878 2709513 0.023526229662238593 0.1899877698683677 chr14 107349540 4589926 0.0427568296985716 0.3234313110813559 chr15 102531392 6116640 0.05965626605361995 0.31227335219146274 chr16 90354753 4503193 0.0498390272839327 0.32261638530133957 chr17 81195210 3994312 0.04919393644033928 0.34816665639246436 chr18 78077248 6408498 0.08207894315127501 1.009975840147967 chr19 59128983 1372394 0.023210174272742017 0.5110802686674348 chr20 63025520 4523001 0.07176459630955842 0.34639574747037094 chr21 48129895 1870014 0.038853481812083736 0.3155242489930412 chr22 51304566 2036584 0.03969596000480737 0.24946671290295103 chrMT 16571 25035 1.5107718303059563 1.9455987180935084 chrX 155270560 5430113 0.03497194188003186 0.27896360915762997 chrY 59373566 461398 0.007771101368578738 0.3302483628908417