BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618637.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 26,474,022 number of mapped reads = 18,861,721 (71.25%) number of supplementary alignments = 172,340 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,629,050 number of mapped paired reads (second in pair) = 9,232,671 number of mapped paired reads (both in pair) = 18,052,070 number of mapped paired reads (singletons) = 809,651 number of mapped bases = 1,739,897,362 bp number of sequenced bases = 1,738,682,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,308,597 duplication rate = 32.65% >>>>>>> Insert size mean insert size = 184,581.7484 std insert size = 4,290,535.2388 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.0824 >>>>>>> ACTG content number of A's = 463,483,011 bp (26.66%) number of C's = 386,090,472 bp (22.21%) number of T's = 473,485,241 bp (27.23%) number of G's = 414,430,437 bp (23.84%) number of N's = 1,193,613 bp (0.07%) GC percentage = 46.04% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 24,678,253 number of insertions = 338,722 mapped reads with insertion percentage = 1.77% number of deletions = 871,544 mapped reads with deletion percentage = 4.5% homopolymer indels = 51.7% >>>>>>> Coverage mean coverageData = 0.562X std coverageData = 2.8009X There is a 15.95% of reference with a coverageData >= 1X There is a 9.64% of reference with a coverageData >= 2X There is a 6.51% of reference with a coverageData >= 3X There is a 4.74% of reference with a coverageData >= 4X There is a 3.54% of reference with a coverageData >= 5X There is a 2.74% of reference with a coverageData >= 6X There is a 2.14% of reference with a coverageData >= 7X There is a 1.71% of reference with a coverageData >= 8X There is a 1.38% of reference with a coverageData >= 9X There is a 1.13% of reference with a coverageData >= 10X There is a 0.92% of reference with a coverageData >= 11X There is a 0.76% of reference with a coverageData >= 12X There is a 0.63% of reference with a coverageData >= 13X There is a 0.53% of reference with a coverageData >= 14X There is a 0.45% of reference with a coverageData >= 15X There is a 0.38% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 153289320 0.6150007546019314 5.3055971772180515 chr2 243199373 144646484 0.5947650366680839 2.9329465869202958 chr3 198022430 108938099 0.5501300988983925 2.133773302066568 chr4 191154276 86788921 0.4540255275273047 1.9946987422882734 chr5 180915260 96024148 0.5307686482610698 2.1368869194924303 chr6 171115067 93405564 0.5458640529883906 2.398190339284513 chr7 159138663 87785063 0.5516262443401325 2.410130540172964 chr8 146364022 85841572 0.5864936671390459 2.4395806789406267 chr9 141213431 74573634 0.5280916515653529 2.5542079321888513 chr10 135534747 89075877 0.6572180121456235 2.4782850915570473 chr11 135006516 88893630 0.6584395526509254 2.628253474841667 chr12 133851895 77676184 0.5803144139274233 2.606929838836502 chr13 115169878 45925143 0.3987600212618094 1.8238963303922713 chr14 107349540 54622400 0.5088275180312836 2.2197117676621665 chr15 102531392 56898796 0.5549402469830899 2.2263059721284058 chr16 90354753 61283618 0.6782556087558559 3.840257078905101 chr17 81195210 57958669 0.7138188201003483 2.6880498457651125 chr18 78077248 43060089 0.5515062339287369 2.346919128281278 chr19 59128983 38264838 0.6471418255240412 2.6779092468724532 chr20 63025520 49631268 0.7874789133036904 2.716855517227307 chr21 48129895 22520168 0.46790395034105103 3.179986539066565 chr22 51304566 32039169 0.6244896214500675 2.6071889455341477 chrMT 16571 1371 0.08273489831633576 0.6232849477956219 chrX 155270560 87979775 0.5666223848229825 2.094804535039025 chrY 59373566 2773562 0.04671375136874885 1.3366994500295908