BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975303.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 50,248,508 number of mapped reads = 50,082,060 (99.67%) number of supplementary alignments = 96,821 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,033,660 number of mapped paired reads (second in pair) = 25,048,400 number of mapped paired reads (both in pair) = 50,007,202 number of mapped paired reads (singletons) = 74,858 number of mapped bases = 4,554,129,133 bp number of sequenced bases = 4,552,538,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,195,749 duplication rate = 42.91% >>>>>>> Insert size mean insert size = 32,684.5198 std insert size = 1,774,537.8736 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 55.5681 >>>>>>> ACTG content number of A's = 1,200,752,443 bp (26.38%) number of C's = 1,027,375,294 bp (22.57%) number of T's = 1,228,486,958 bp (26.98%) number of G's = 1,095,840,461 bp (24.07%) number of N's = 83,159 bp (0%) GC percentage = 46.64% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 27,951,742 number of insertions = 389,773 mapped reads with insertion percentage = 0.77% number of deletions = 1,074,075 mapped reads with deletion percentage = 2.11% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 1.4711X std coverageData = 23.0622X There is a 13.89% of reference with a coverageData >= 1X There is a 7.69% of reference with a coverageData >= 2X There is a 4.45% of reference with a coverageData >= 3X There is a 3.19% of reference with a coverageData >= 4X There is a 2.38% of reference with a coverageData >= 5X There is a 1.99% of reference with a coverageData >= 6X There is a 1.71% of reference with a coverageData >= 7X There is a 1.54% of reference with a coverageData >= 8X There is a 1.42% of reference with a coverageData >= 9X There is a 1.33% of reference with a coverageData >= 10X There is a 1.26% of reference with a coverageData >= 11X There is a 1.2% of reference with a coverageData >= 12X There is a 1.15% of reference with a coverageData >= 13X There is a 1.11% of reference with a coverageData >= 14X There is a 1.07% of reference with a coverageData >= 15X There is a 1.04% of reference with a coverageData >= 16X There is a 1.01% of reference with a coverageData >= 17X There is a 0.98% of reference with a coverageData >= 18X There is a 0.95% of reference with a coverageData >= 19X There is a 0.93% of reference with a coverageData >= 20X There is a 0.91% of reference with a coverageData >= 21X There is a 0.88% of reference with a coverageData >= 22X There is a 0.86% of reference with a coverageData >= 23X There is a 0.84% of reference with a coverageData >= 24X There is a 0.83% of reference with a coverageData >= 25X There is a 0.81% of reference with a coverageData >= 26X There is a 0.79% of reference with a coverageData >= 27X There is a 0.78% of reference with a coverageData >= 28X There is a 0.76% of reference with a coverageData >= 29X There is a 0.75% of reference with a coverageData >= 30X There is a 0.73% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.71% of reference with a coverageData >= 33X There is a 0.69% of reference with a coverageData >= 34X There is a 0.68% of reference with a coverageData >= 35X There is a 0.67% of reference with a coverageData >= 36X There is a 0.66% of reference with a coverageData >= 37X There is a 0.65% of reference with a coverageData >= 38X There is a 0.64% of reference with a coverageData >= 39X There is a 0.63% of reference with a coverageData >= 40X There is a 0.62% of reference with a coverageData >= 41X There is a 0.61% of reference with a coverageData >= 42X There is a 0.6% of reference with a coverageData >= 43X There is a 0.59% of reference with a coverageData >= 44X There is a 0.58% of reference with a coverageData >= 45X There is a 0.57% of reference with a coverageData >= 46X There is a 0.56% of reference with a coverageData >= 47X There is a 0.55% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 554858348 2.2261061808949316 31.815659774078373 chr2 243199373 329471959 1.3547401662092278 19.93013986963759 chr3 198022430 237927028 1.2015155454864381 18.52122829630854 chr4 191154276 200477080 1.0487710983771035 17.876953387636732 chr5 180915260 221440236 1.2239997665205247 19.396261562335905 chr6 171115067 353373317 2.065120992530716 33.46491185393667 chr7 159138663 254238132 1.5975887141894614 27.503343820883423 chr8 146364022 164568840 1.124380416384021 17.296168584539988 chr9 141213431 187883949 1.3304963109351828 20.41218140538436 chr10 135534747 207692182 1.5323906717441247 23.286689870213014 chr11 135006516 219052380 1.622531908015462 23.15375856877742 chr12 133851895 256309264 1.9148721353552747 27.076028706917043 chr13 115169878 89750944 0.7792918214257377 13.430341526397035 chr14 107349540 154892013 1.4428754235928725 21.12838468261116 chr15 102531392 166373219 1.6226563958090026 23.093449849199693 chr16 90354753 150617616 1.6669584166756561 22.808359919967472 chr17 81195210 184380288 2.2708271584001074 27.23481134945453 chr18 78077248 75546190 0.9675826432816894 17.175958816582458 chr19 59128983 179414374 3.03428817640919 34.31333366653123 chr20 63025520 122578055 1.9448955756334894 27.190633361171496 chr21 48129895 46646501 0.9691793634704584 18.41051826182021 chr22 51304566 77901064 1.5184041124136982 22.775286262195458 chrMT 16571 147617 8.908152797055097 13.238725137218047 chrX 155270560 116780996 0.7521129311313104 13.4509434229236 chrY 59373566 1807541 0.030443531048817245 1.6733733269659048