BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975220.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/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 = 51,951,140 number of mapped reads = 51,784,744 (99.68%) number of supplementary alignments = 107,582 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,887,827 number of mapped paired reads (second in pair) = 25,896,917 number of mapped paired reads (both in pair) = 51,717,784 number of mapped paired reads (singletons) = 66,960 number of mapped bases = 4,745,224,874 bp number of sequenced bases = 4,743,461,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,922,611 duplication rate = 40.49% >>>>>>> Insert size mean insert size = 54,458.8872 std insert size = 2,395,004.6851 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 55.8039 >>>>>>> ACTG content number of A's = 1,259,382,349 bp (26.55%) number of C's = 1,065,921,313 bp (22.47%) number of T's = 1,270,352,468 bp (26.78%) number of G's = 1,147,615,014 bp (24.19%) number of N's = 190,182 bp (0%) GC percentage = 46.67% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 33,531,950 number of insertions = 506,237 mapped reads with insertion percentage = 0.97% number of deletions = 1,249,504 mapped reads with deletion percentage = 2.38% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 1.5328X std coverageData = 22.1459X There is a 13.58% of reference with a coverageData >= 1X There is a 6.86% of reference with a coverageData >= 2X There is a 3.92% of reference with a coverageData >= 3X There is a 2.92% of reference with a coverageData >= 4X There is a 2.31% of reference with a coverageData >= 5X There is a 2.02% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.68% of reference with a coverageData >= 8X There is a 1.58% of reference with a coverageData >= 9X There is a 1.5% of reference with a coverageData >= 10X There is a 1.44% of reference with a coverageData >= 11X There is a 1.38% of reference with a coverageData >= 12X There is a 1.33% of reference with a coverageData >= 13X There is a 1.28% of reference with a coverageData >= 14X There is a 1.24% of reference with a coverageData >= 15X There is a 1.2% of reference with a coverageData >= 16X There is a 1.17% of reference with a coverageData >= 17X There is a 1.14% of reference with a coverageData >= 18X There is a 1.11% of reference with a coverageData >= 19X There is a 1.08% of reference with a coverageData >= 20X There is a 1.05% of reference with a coverageData >= 21X There is a 1.03% of reference with a coverageData >= 22X There is a 1% of reference with a coverageData >= 23X There is a 0.98% of reference with a coverageData >= 24X There is a 0.96% of reference with a coverageData >= 25X There is a 0.93% of reference with a coverageData >= 26X There is a 0.92% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.88% of reference with a coverageData >= 29X There is a 0.86% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.81% of reference with a coverageData >= 33X There is a 0.8% of reference with a coverageData >= 34X There is a 0.78% of reference with a coverageData >= 35X There is a 0.77% of reference with a coverageData >= 36X There is a 0.75% of reference with a coverageData >= 37X There is a 0.74% of reference with a coverageData >= 38X There is a 0.73% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.7% of reference with a coverageData >= 41X There is a 0.69% of reference with a coverageData >= 42X There is a 0.68% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.66% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.64% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.61% of reference with a coverageData >= 50X There is a 0.6% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 741764177 2.975977247414762 36.219898468682246 chr2 243199373 307135217 1.262894773170324 16.86781164123836 chr3 198022430 286497004 1.4467906691176349 20.659608143641737 chr4 191154276 155544575 0.8137122446583408 12.388190542528323 chr5 180915260 194918575 1.077402619325755 15.580673723549074 chr6 171115067 311745400 1.8218465823351488 25.733500632526233 chr7 159138663 243874317 1.532464282422682 21.46281953286559 chr8 146364022 198474922 1.35603626689078 19.8300052785488 chr9 141213431 158123781 1.119750294856868 15.88019953423504 chr10 135534747 125696919 0.927414716758943 13.179393508575373 chr11 135006516 269389867 1.9953841857529306 25.563587030220063 chr12 133851895 292941595 2.1885502256056966 26.81605325989214 chr13 115169878 50250289 0.4363145109869787 7.599785193860719 chr14 107349540 130983159 1.2201557547428707 17.06292090576462 chr15 102531392 99983272 0.9751479039707176 14.200895391019431 chr16 90354753 132750482 1.469214154124244 20.56238948583556 chr17 81195210 260003017 3.202196496566731 34.36374731030259 chr18 78077248 94256506 1.2072211612786352 18.11893097365438 chr19 59128983 272861371 4.6146806042647475 46.563436749982294 chr20 63025520 134824479 2.139204547618171 26.86393591187579 chr21 48129895 63165421 1.3123947392779478 20.990130533799917 chr22 51304566 49356166 0.962022873363747 14.141737703851744 chrMT 16571 91524 5.523142839901032 7.265953900223275 chrX 155270560 162167833 1.0444209964851032 17.986891213336264 chrY 59373566 8425006 0.14189826496188557 3.6210535500471814