BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082330.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,367,430 number of mapped reads = 2,140,068 (90.4%) number of supplementary alignments = 17,238 (0.73%) number of secondary alignments = 0 number of mapped bases = 145,569,651 bp number of sequenced bases = 145,515,098 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,852 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1182 >>>>>>> ACTG content number of A's = 41,488,276 bp (28.51%) number of C's = 27,301,007 bp (18.76%) number of T's = 44,911,967 bp (30.86%) number of G's = 31,810,951 bp (21.86%) number of N's = 2,897 bp (0%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,221,760 number of insertions = 11,948 mapped reads with insertion percentage = 0.55% number of deletions = 33,416 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.047X std coverageData = 0.4088X There is a 4.11% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 11918838 0.04781868928623452 0.6881229639331529 chr2 243199373 12602051 0.05181777750718132 0.49574212886129154 chr3 198022430 10427070 0.052656004675833944 0.2548875153217883 chr4 191154276 9929291 0.051943860256623293 0.261979725112001 chr5 180915260 9677562 0.053492237194363815 0.25672558089043707 chr6 171115067 7572390 0.04425320419037092 0.2694355450880682 chr7 159138663 8103302 0.05091975669042789 0.5582209246122602 chr8 146364022 6887587 0.04705792383868763 0.7233214932562411 chr9 141213431 5914639 0.04188439412678813 0.3603264702448669 chr10 135534747 7208212 0.05318349839838488 0.3853018177206148 chr11 135006516 6272573 0.04646126117349773 0.3336692977352409 chr12 133851895 6998819 0.0522877841961072 0.2574157473784926 chr13 115169878 4685306 0.04068169630256967 0.22220237658193243 chr14 107349540 4160508 0.03875664488175729 0.2355933689524643 chr15 102531392 4090297 0.03989311878258709 0.22386459968272976 chr16 90354753 3327513 0.0368272048732179 0.24544146369174197 chr17 81195210 3629967 0.04470666434633275 0.25445561720854065 chr18 78077248 3589453 0.04597309833461343 0.6516245741915474 chr19 59128983 2695504 0.045586848669458765 0.5240360449514566 chr20 63025520 2836791 0.04501019586986351 0.24160106974000728 chr21 48129895 1878716 0.03903428420111866 0.23550303637266629 chr22 51304566 1501743 0.029271137387654737 0.1878454576990392 chrMT 16571 15484 0.9344034759519643 0.9993753102586944 chrX 155270560 9287689 0.059816162188118596 0.3059417992338504 chrY 59373566 358346 0.0060354468182018915 0.1281810985751177