BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013279.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 = 1,644,238 number of mapped reads = 1,352,660 (82.27%) number of supplementary alignments = 17,918 (1.09%) number of secondary alignments = 0 number of mapped bases = 84,774,214 bp number of sequenced bases = 84,700,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,014 duplication rate = 8.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2625 >>>>>>> ACTG content number of A's = 23,709,317 bp (27.99%) number of C's = 14,897,355 bp (17.59%) number of T's = 27,691,187 bp (32.69%) number of G's = 18,384,833 bp (21.71%) number of N's = 17,689 bp (0.02%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 844,417 number of insertions = 6,483 mapped reads with insertion percentage = 0.48% number of deletions = 42,396 mapped reads with deletion percentage = 3.08% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.299X There is a 1.83% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 4397968 0.017644762457783406 0.36219713334789194 chr2 243199373 14281207 0.05872221964980148 0.468812921039396 chr3 198022430 5133174 0.025922184673726104 0.22612480637641003 chr4 191154276 3695094 0.019330428161596552 0.22842163130371124 chr5 180915260 5212777 0.028813362675984326 0.24062466603407628 chr6 171115067 2230084 0.0130326571417583 0.1830107193561017 chr7 159138663 4481350 0.02816003298959474 0.3209221054510195 chr8 146364022 4337736 0.029636627503991386 0.36400915265941086 chr9 141213431 3773046 0.026718747453986866 0.27787581097065706 chr10 135534747 5436029 0.040108010088365016 0.43558329118529204 chr11 135006516 2335502 0.01729917984106782 0.20772952439745143 chr12 133851895 4946624 0.036955950455538934 0.27403121970163347 chr13 115169878 2814368 0.02443666737234887 0.22179136081934234 chr14 107349540 3505595 0.03265589214448427 0.2622800490911327 chr15 102531392 2284932 0.022285194372470823 0.2043145517054922 chr16 90354753 2323058 0.025710412821337687 0.23661105363400775 chr17 81195210 1003779 0.012362539612866326 0.1581485163508165 chr18 78077248 2042686 0.02616237191146901 0.42002904034094707 chr19 59128983 1068331 0.01806780610449532 0.33490644155998156 chr20 63025520 905508 0.014367322951083943 0.16749826003125534 chr21 48129895 1515634 0.031490490473748176 0.2696027601282353 chr22 51304566 761175 0.01483639877199234 0.1652127520819529 chrMT 16571 9468 0.5713596041276929 0.9616542152573561 chrX 155270560 5999157 0.038636796312192086 0.2840572415406304 chrY 59373566 279932 0.004714758079378287 0.1648779498981561