BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927042.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 17,912,276 number of mapped reads = 17,314,706 (96.66%) number of supplementary alignments = 686,990 (3.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,705,739 number of mapped paired reads (second in pair) = 8,608,967 number of mapped paired reads (both in pair) = 16,970,202 number of mapped paired reads (singletons) = 344,504 number of mapped bases = 1,549,175,728 bp number of sequenced bases = 1,547,997,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,455,051 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 392,772.4143 std insert size = 6,126,300.7613 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.44 >>>>>>> ACTG content number of A's = 444,336,825 bp (28.7%) number of C's = 295,272,746 bp (19.07%) number of T's = 457,783,467 bp (29.57%) number of G's = 350,439,808 bp (22.64%) number of N's = 164,195 bp (0.01%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 16,861,626 number of insertions = 267,262 mapped reads with insertion percentage = 1.52% number of deletions = 812,191 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.8% >>>>>>> Coverage mean coverageData = 0.5004X std coverageData = 1.8651X There is a 25.43% of reference with a coverageData >= 1X There is a 11.61% of reference with a coverageData >= 2X There is a 5.46% of reference with a coverageData >= 3X There is a 2.86% of reference with a coverageData >= 4X There is a 1.57% of reference with a coverageData >= 5X There is a 0.91% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 127604904 0.5119542069265296 2.204566073134242 chr2 243199373 141329302 0.5811252728846468 3.1039720560701274 chr3 198022430 106315378 0.5368855336236406 1.2164530963235711 chr4 191154276 93587572 0.4895918310506431 1.5044530628424608 chr5 180915260 99977730 0.5526218739093651 1.213401482003797 chr6 171115067 92675115 0.5415952938849038 1.2216678844376414 chr7 159138663 79681116 0.5007024345805896 1.4512944975798034 chr8 146364022 75014173 0.5125178440368358 1.303396806447119 chr9 141213431 67623312 0.4788730896284221 2.178134509942351 chr10 135534747 71366605 0.5265557842521372 3.7516215716409724 chr11 135006516 74910440 0.5548653666464514 1.6116214507669722 chr12 133851895 70515655 0.5268185033913789 1.2002198783503533 chr13 115169878 49714199 0.4316597348483776 1.0724288184248068 chr14 107349540 46370476 0.4319578453712983 1.1111419958821098 chr15 102531392 41445822 0.4042256833887518 1.0478727838186175 chr16 90354753 43916732 0.48604783414105507 2.378643807044471 chr17 81195210 38535320 0.4746009031813576 1.3251322564265453 chr18 78077248 42571170 0.5452442432397208 2.0748819099993367 chr19 59128983 23076062 0.39026651278612384 1.4539404047356321 chr20 63025520 34829369 0.5526232707005035 1.289124816307511 chr21 48129895 20705994 0.4302106622090075 1.4382337075045117 chr22 51304566 17106589 0.3334320964726609 1.0053065327457498 chrMT 16571 82739 4.992999818960835 4.872762449552827 chrX 155270560 87434228 0.563108859786427 1.3037487438728494 chrY 59373566 2785726 0.046918623685159824 1.9596922888542991