BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617483.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 = 30,517,873 (95.37%) number of supplementary alignments = 135,725 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,427,594 number of mapped paired reads (second in pair) = 15,090,279 number of mapped paired reads (both in pair) = 29,929,776 number of mapped paired reads (singletons) = 588,097 number of mapped bases = 2,974,538,977 bp number of sequenced bases = 2,972,766,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,314,099 duplication rate = 10.02% >>>>>>> Insert size mean insert size = 29,550.4659 std insert size = 1,585,614.7671 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.7781 >>>>>>> ACTG content number of A's = 875,336,648 bp (29.45%) number of C's = 600,879,000 bp (20.21%) number of T's = 875,633,774 bp (29.46%) number of G's = 615,710,813 bp (20.71%) number of N's = 5,206,052 bp (0.18%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 33,282,067 number of insertions = 441,760 mapped reads with insertion percentage = 1.42% number of deletions = 1,038,416 mapped reads with deletion percentage = 3.33% homopolymer indels = 47.51% >>>>>>> Coverage mean coverageData = 0.9609X std coverageData = 9.6897X There is a 38.3% of reference with a coverageData >= 1X There is a 20.65% of reference with a coverageData >= 2X There is a 11.66% of reference with a coverageData >= 3X There is a 6.93% of reference with a coverageData >= 4X There is a 4.27% of reference with a coverageData >= 5X There is a 2.74% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.24% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% 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 191586382 0.7686495673766045 9.44148757768964 chr2 243199373 307455407 1.2642113472883008 11.426708596309545 chr3 198022430 246109513 1.2428365463447753 2.231826624530205 chr4 191154276 153824810 0.8047155063379278 6.178238259613856 chr5 180915260 190465404 1.0527879406082163 2.0700882543821066 chr6 171115067 140386590 0.8204221431885949 5.3871077665199 chr7 159138663 229330512 1.4410735120980624 13.145804068341652 chr8 146364022 132129729 0.9027473226992901 3.8241621564024153 chr9 141213431 123055918 0.8714179460734156 18.4363918920641 chr10 135534747 125711039 0.9275188966855857 18.542285267127372 chr11 135006516 167899022 1.2436364330740894 12.535969688950699 chr12 133851895 129929820 0.9706983976580982 1.9755574216114453 chr13 115169878 126050180 1.0944717680433769 2.106601959809493 chr14 107349540 86568897 0.8064207541084946 2.215828799721833 chr15 102531392 67041970 0.6538677442319324 1.4437333903875238 chr16 90354753 80182728 0.8874212516523619 14.778841347754211 chr17 81195210 82893347 1.020914250976135 13.604741793134343 chr18 78077248 53372000 0.6835794212418962 17.137297782184778 chr19 59128983 35609351 0.6022317515591297 5.970968463113871 chr20 63025520 87910531 1.3948402329722944 2.783965556539355 chr21 48129895 42857027 0.8904450549912897 3.8067956200042152 chr22 51304566 22228771 0.4332708125822563 1.2459423062452213 chrMT 16571 2110136 127.33908635568162 91.58321131504064 chrX 155270560 139586480 0.8989887071960068 4.035869259090458 chrY 59373566 10243413 0.1725248067464905 13.752608300985628