BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927001.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,343,678 number of mapped reads = 30,854,178 (98.44%) number of supplementary alignments = 335,118 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,468,538 number of mapped paired reads (second in pair) = 15,385,640 number of mapped paired reads (both in pair) = 30,550,508 number of mapped paired reads (singletons) = 303,670 number of mapped bases = 2,888,444,908 bp number of sequenced bases = 2,886,248,121 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,601,928 duplication rate = 6.52% >>>>>>> Insert size mean insert size = 101,428.6577 std insert size = 3,092,767.9435 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.5921 >>>>>>> ACTG content number of A's = 828,330,206 bp (28.7%) number of C's = 568,206,830 bp (19.69%) number of T's = 842,143,377 bp (29.18%) number of G's = 647,245,497 bp (22.43%) number of N's = 322,211 bp (0.01%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 26,399,187 number of insertions = 477,662 mapped reads with insertion percentage = 1.52% number of deletions = 1,546,278 mapped reads with deletion percentage = 4.88% homopolymer indels = 52.99% >>>>>>> Coverage mean coverageData = 0.9331X std coverageData = 3.8513X There is a 34.25% of reference with a coverageData >= 1X There is a 20.14% of reference with a coverageData >= 2X There is a 12.29% of reference with a coverageData >= 3X There is a 7.89% of reference with a coverageData >= 4X There is a 5.2% of reference with a coverageData >= 5X There is a 3.51% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 1.68% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.84% of reference with a coverageData >= 10X There is a 0.61% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 243178676 0.9756391981065515 5.806265411686377 chr2 243199373 259147551 1.0655765588671975 6.26309552450931 chr3 198022430 200322755 1.0116164870817916 1.9913972040672008 chr4 191154276 179174569 0.937329641529965 3.4495313092441635 chr5 180915260 183098708 1.0120688989972433 1.9582817845905887 chr6 171115067 174039919 1.0170928957413201 3.4375234244948896 chr7 159138663 152782935 0.960061697891731 2.7906688788035585 chr8 146364022 153219881 1.046841149254562 2.4161650391551768 chr9 141213431 54284471 0.38441436211545627 4.876686533876888 chr10 135534747 144007000 1.0625098226656224 6.390483130239556 chr11 135006516 136896622 1.0140001094465692 3.417807089436861 chr12 133851895 132775260 0.9919565203017858 2.012620569473572 chr13 115169878 93355344 0.8105881991122713 1.7710748057203196 chr14 107349540 90091240 0.8392326599629584 1.8870621710710287 chr15 102531392 85989064 0.8386608464264291 1.8933147247670694 chr16 90354753 91346680 1.0109781385822614 4.316093214268219 chr17 81195210 74464019 0.9170986687515187 2.596636766761492 chr18 78077248 78601842 1.0067189099697775 5.443586961351871 chr19 59128983 46631083 0.788633266362792 3.616905948838943 chr20 63025520 66634305 1.0572591071045507 2.295152621746986 chr21 48129895 38167130 0.7930025610901499 3.1095622658907414 chr22 51304566 33942626 0.6615907441844455 1.712681138745325 chrMT 16571 313523 18.919980689155754 17.156085315212316 chrX 155270560 170717921 1.0994867346392 2.4436138401171013 chrY 59373566 5261784 0.08862166035302646 3.3416319058627684