BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618641.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 = 61,115,288 number of mapped reads = 52,001,213 (85.09%) number of supplementary alignments = 155,288 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,932,267 number of mapped paired reads (second in pair) = 24,068,946 number of mapped paired reads (both in pair) = 47,276,502 number of mapped paired reads (singletons) = 4,724,711 number of mapped bases = 4,884,939,447 bp number of sequenced bases = 4,881,553,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,917,899 duplication rate = 17.61% >>>>>>> Insert size mean insert size = 123,333.9126 std insert size = 3,546,631.9318 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 53.0686 >>>>>>> ACTG content number of A's = 1,321,188,798 bp (27.06%) number of C's = 1,086,090,280 bp (22.25%) number of T's = 1,353,314,094 bp (27.72%) number of G's = 1,120,734,482 bp (22.96%) number of N's = 226,000 bp (0%) GC percentage = 45.21% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 71,198,495 number of insertions = 899,387 mapped reads with insertion percentage = 1.7% number of deletions = 2,440,543 mapped reads with deletion percentage = 4.57% homopolymer indels = 52.44% >>>>>>> Coverage mean coverageData = 1.578X std coverageData = 7.5338X There is a 25.61% of reference with a coverageData >= 1X There is a 17.42% of reference with a coverageData >= 2X There is a 13.14% of reference with a coverageData >= 3X There is a 10.49% of reference with a coverageData >= 4X There is a 8.64% of reference with a coverageData >= 5X There is a 7.28% of reference with a coverageData >= 6X There is a 6.24% of reference with a coverageData >= 7X There is a 5.42% of reference with a coverageData >= 8X There is a 4.75% of reference with a coverageData >= 9X There is a 4.2% of reference with a coverageData >= 10X There is a 3.74% of reference with a coverageData >= 11X There is a 3.36% of reference with a coverageData >= 12X There is a 3.02% of reference with a coverageData >= 13X There is a 2.74% of reference with a coverageData >= 14X There is a 2.49% of reference with a coverageData >= 15X There is a 2.27% of reference with a coverageData >= 16X There is a 2.07% of reference with a coverageData >= 17X There is a 1.9% of reference with a coverageData >= 18X There is a 1.75% of reference with a coverageData >= 19X There is a 1.62% of reference with a coverageData >= 20X There is a 1.49% of reference with a coverageData >= 21X There is a 1.38% of reference with a coverageData >= 22X There is a 1.29% of reference with a coverageData >= 23X There is a 1.2% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.04% of reference with a coverageData >= 26X There is a 0.97% of reference with a coverageData >= 27X There is a 0.91% of reference with a coverageData >= 28X There is a 0.85% of reference with a coverageData >= 29X There is a 0.8% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.71% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.63% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.56% of reference with a coverageData >= 36X There is a 0.53% of reference with a coverageData >= 37X There is a 0.5% of reference with a coverageData >= 38X There is a 0.47% of reference with a coverageData >= 39X There is a 0.45% of reference with a coverageData >= 40X There is a 0.43% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.37% of reference with a coverageData >= 44X There is a 0.35% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.32% of reference with a coverageData >= 47X There is a 0.3% of reference with a coverageData >= 48X There is a 0.29% of reference with a coverageData >= 49X There is a 0.28% of reference with a coverageData >= 50X There is a 0.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 452390822 1.8150037909032932 8.186442913184553 chr2 243199373 429454171 1.7658522951866327 9.256593375437955 chr3 198022430 320790122 1.6199686166865037 6.293442800004081 chr4 191154276 254192648 1.3297774620537393 6.226919746843329 chr5 180915260 283150835 1.5651019985820986 6.951791479407463 chr6 171115067 275175495 1.6081312991567247 6.3125902782647385 chr7 159138663 246068077 1.5462494931228623 6.330899104614129 chr8 146364022 247837248 1.6932935062415817 6.94824122251617 chr9 141213431 220306660 1.5600970703700274 7.183552316631545 chr10 135534747 252164074 1.8605123747344288 7.41167090334298 chr11 135006516 251033176 1.859415259630876 7.7306466344940485 chr12 133851895 227117288 1.696780519991891 7.659145071643293 chr13 115169878 137313422 1.1922685374382354 5.399615489533833 chr14 107349540 153718735 1.4319459123904956 6.232811274519442 chr15 102531392 165950966 1.6185381156241399 7.189027301857047 chr16 90354753 178110578 1.9712363997055031 14.920593827201607 chr17 81195210 173993583 2.142904526018222 8.617422479273712 chr18 78077248 130846633 1.6758612316868546 7.09963963305619 chr19 59128983 106322940 1.798152692732767 7.4732991794978565 chr20 63025520 153198802 2.4307423722961747 8.614772588192428 chr21 48129895 66225149 1.3759670367034875 9.963526895569297 chr22 51304566 95855290 1.8683578767628597 8.279233368100176 chrMT 16571 11356 0.685293585178927 1.9991688244538293 chrX 155270560 19801657 0.1275300159927291 2.8710884960656826 chrY 59373566 43909720 0.7395499876157009 6.14460146493245