BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617496.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,280,258 (94.63%) number of supplementary alignments = 140,356 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,211,589 number of mapped paired reads (second in pair) = 15,068,669 number of mapped paired reads (both in pair) = 29,759,770 number of mapped paired reads (singletons) = 520,488 number of mapped bases = 2,948,958,040 bp number of sequenced bases = 2,947,235,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,139,429 duplication rate = 9.79% >>>>>>> Insert size mean insert size = 30,818.0935 std insert size = 1,634,530.6695 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 52.7298 >>>>>>> ACTG content number of A's = 871,050,564 bp (29.55%) number of C's = 595,134,887 bp (20.19%) number of T's = 869,225,767 bp (29.49%) number of G's = 609,859,821 bp (20.69%) number of N's = 1,964,236 bp (0.07%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 39,304,680 number of insertions = 433,749 mapped reads with insertion percentage = 1.4% number of deletions = 1,017,101 mapped reads with deletion percentage = 3.29% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.9526X std coverageData = 9.6469X There is a 38.06% of reference with a coverageData >= 1X There is a 20.5% of reference with a coverageData >= 2X There is a 11.54% of reference with a coverageData >= 3X There is a 6.84% of reference with a coverageData >= 4X There is a 4.21% of reference with a coverageData >= 5X There is a 2.69% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.21% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% 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 189942242 0.7620532347640571 9.37903312100338 chr2 243199373 304587147 1.2524174846454066 11.22671196139625 chr3 198022430 243604339 1.2301855855420014 2.219763213549415 chr4 191154276 152555098 0.7980731647352738 5.960566803875377 chr5 180915260 189042934 1.0449253092304098 2.0710709598143997 chr6 171115067 138991262 0.8122678174213612 5.39210954772774 chr7 159138663 227750992 1.4311480799609333 13.150083374270588 chr8 146364022 130793286 0.8936163697387326 3.8236779316753737 chr9 141213431 122105329 0.8646863696697519 18.164961247192764 chr10 135534747 125032595 0.9225132135304019 18.64144167614599 chr11 135006516 166298337 1.2317800794148335 12.789892877062316 chr12 133851895 129041870 0.9640645730118352 1.9675607335457475 chr13 115169878 125435083 1.0891309878786188 2.105546401733695 chr14 107349540 85754035 0.7988300182748803 2.179521073602936 chr15 102531392 66412096 0.6477245134836364 1.4388036376104434 chr16 90354753 79532131 0.8802207782030017 15.001725510252689 chr17 81195210 82071743 1.0107953782002657 13.611373986155474 chr18 78077248 53003556 0.6788604536881218 16.748212037390264 chr19 59128983 34905231 0.5903235474217441 5.795669005874096 chr20 63025520 86745992 1.3763629716978139 2.756438498228956 chr21 48129895 42518731 0.8834162426491893 3.717896155180363 chr22 51304566 21840241 0.4256978024139216 1.2339808916684651 chrMT 16571 2103299 126.92649809908878 92.83277478202409 chrX 155270560 138732455 0.8934884694175123 4.115361951580458 chrY 59373566 10158016 0.1710865067461166 13.667533091988519