BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094002.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 461,164 number of mapped reads = 202,778 (43.97%) number of supplementary alignments = 304 (0.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 100,800 number of mapped paired reads (second in pair) = 101,978 number of mapped paired reads (both in pair) = 199,212 number of mapped paired reads (singletons) = 3,566 number of mapped bases = 29,788,114 bp number of sequenced bases = 29,781,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,341 duplication rate = 29.7% >>>>>>> Insert size mean insert size = 7,548.6832 std insert size = 841,993.814 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 6.4017 >>>>>>> ACTG content number of A's = 9,070,361 bp (30.46%) number of C's = 5,554,367 bp (18.65%) number of T's = 9,070,304 bp (30.46%) number of G's = 6,085,942 bp (20.44%) number of N's = 522 bp (0%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 417,594 number of insertions = 969 mapped reads with insertion percentage = 0.41% number of deletions = 4,268 mapped reads with deletion percentage = 2.08% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 33.0822X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3447 1.3829454009665235E-5 0.005486898306606421 chr2 243199373 246356 0.0010129795852722038 0.995746547227026 chr3 198022430 2890 1.4594306311663784E-5 0.005316414535723368 chr4 191154276 3087 1.6149259459934864E-5 0.005620678188496707 chr5 180915260 2953 1.6322558970426264E-5 0.005600715801628191 chr6 171115067 3731 2.180404137059421E-5 0.007864273395925018 chr7 159138663 92529 5.814363288951347E-4 0.6719425030959822 chr8 146364022 2029 1.3862696394063289E-5 0.004666292506122233 chr9 141213431 1639 1.160654470607686E-5 0.004201665588151776 chr10 135534747 2908 2.145575259752394E-5 0.009311709394821335 chr11 135006516 8495 6.29228888478242E-5 0.08725402927955166 chr12 133851895 5173 3.864719285446052E-5 0.021653348861477906 chr13 115169878 1919 1.666234290879426E-5 0.0053650068348755475 chr14 107349540 2725 2.538436587618354E-5 0.024199373749640818 chr15 102531392 2692 2.625537357378314E-5 0.011164411853611588 chr16 90354753 2070 2.2909696847934496E-5 0.007122698421472389 chr17 81195210 1898 2.337576317617751E-5 0.010471919408375094 chr18 78077248 1340 1.716249015334147E-5 0.005033248470701538 chr19 59128983 1122 1.8975465889545235E-5 0.005902434294622756 chr20 63025520 1067 1.692965008460065E-5 0.005057336731966958 chr21 48129895 685 1.4232318603645406E-5 0.004302580779299458 chr22 51304566 823 1.604145720675232E-5 0.005717245123637535 chrMT 16571 29296842 1767.9586023776476 14188.36305455275 chrX 155270560 98043 6.314332865161303E-4 0.4831131192133441 chrY 59373566 1651 2.7806987372124492E-5 0.015453452848338139