BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124889.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,933,798 number of mapped reads = 5,749,767 (96.9%) number of supplementary alignments = 6,335 (0.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,906,379 number of mapped paired reads (second in pair) = 2,843,388 number of mapped paired reads (both in pair) = 5,653,098 number of mapped paired reads (singletons) = 96,669 number of mapped bases = 372,094,454 bp number of sequenced bases = 371,948,896 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 312,245 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 39,921.9922 std insert size = 1,915,492.4561 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 51.9432 >>>>>>> ACTG content number of A's = 104,741,738 bp (28.16%) number of C's = 67,333,274 bp (18.1%) number of T's = 111,601,535 bp (30%) number of G's = 88,269,063 bp (23.73%) number of N's = 3,286 bp (0%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 2,406,665 number of insertions = 38,598 mapped reads with insertion percentage = 0.67% number of deletions = 100,206 mapped reads with deletion percentage = 1.73% homopolymer indels = 50.15% >>>>>>> Coverage mean coverageData = 0.1202X std coverageData = 0.9401X There is a 9.09% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 37422938 0.15014180446114114 1.2618307331361136 chr2 243199373 31843249 0.13093474957273019 1.002030499342189 chr3 198022430 23181908 0.11706708174422463 0.41690356352609925 chr4 191154276 15049761 0.07873096702267858 0.4061780929099613 chr5 180915260 20090915 0.11105152213251662 0.400436828402443 chr6 171115067 21314133 0.12456023524801589 0.7636539199543148 chr7 159138663 22162159 0.13926319715278743 1.7263757804776787 chr8 146364022 27140996 0.18543488781689807 0.6652452897367511 chr9 141213431 14247157 0.10089094853874063 0.877587209078914 chr10 135534747 15571080 0.11488625865070601 1.9642449222585372 chr11 135006516 23741917 0.17585756379343942 0.7513833954440846 chr12 133851895 11680572 0.08726489826684934 0.3568908697076684 chr13 115169878 17923548 0.15562704685681789 0.6324973515748666 chr14 107349540 5927289 0.055214852341239656 0.32571744081635157 chr15 102531392 7571986 0.07385041646562254 0.33079832813725224 chr16 90354753 10852551 0.12011046059746298 1.387367551512634 chr17 81195210 7795542 0.0960098754594021 1.0709828745926122 chr18 78077248 9633749 0.12338740474049495 1.2900262029400356 chr19 59128983 4823360 0.08157353222192237 0.895623569895687 chr20 63025520 9234651 0.14652240870047561 0.47513448057385665 chr21 48129895 3109217 0.06460053569616139 0.3346656730653371 chr22 51304566 2466894 0.048083322642277104 0.2554989372906439 chrMT 16571 6522 0.39357914428821433 0.699011085355456 chrX 155270560 28672828 0.1846636477642639 0.7526306060188317 chrY 59373566 629532 0.010602900287309676 0.35639294727159515