BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089711.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,638,886 number of mapped reads = 18,300,096 (84.57%) number of supplementary alignments = 927 (0%) number of secondary alignments = 0 number of mapped bases = 867,009,784 bp number of sequenced bases = 866,846,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,057,363 duplication rate = 13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1406 >>>>>>> ACTG content number of A's = 253,124,640 bp (29.2%) number of C's = 177,260,834 bp (20.45%) number of T's = 251,813,083 bp (29.05%) number of G's = 184,582,692 bp (21.29%) number of N's = 65,181 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 3,955,446 number of insertions = 34,347 mapped reads with insertion percentage = 0.19% number of deletions = 109,019 mapped reads with deletion percentage = 0.59% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.2801X std coverageData = 1.9877X There is a 11.43% of reference with a coverageData >= 1X There is a 6.02% of reference with a coverageData >= 2X There is a 3.55% of reference with a coverageData >= 3X There is a 2.21% of reference with a coverageData >= 4X There is a 1.41% of reference with a coverageData >= 5X There is a 0.92% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 68950330 0.2766305244230465 3.866915778152512 chr2 243199373 73229798 0.3011101430759034 1.8698657014000406 chr3 198022430 58388821 0.294859632820383 1.1012442848919062 chr4 191154276 56569341 0.29593552487415975 1.2700405787308364 chr5 180915260 53582135 0.2961725561458995 1.1337555221051212 chr6 171115067 50429240 0.294709524322601 1.2821437462976588 chr7 159138663 47886132 0.3009082211530205 2.7240010621073805 chr8 146364022 44609124 0.304782031748212 2.6588912577007378 chr9 141213431 36334891 0.25730478144107977 1.717883476961248 chr10 135534747 40624833 0.2997374023946789 1.779811781971459 chr11 135006516 39980617 0.2961384249038765 1.907617065066731 chr12 133851895 39147107 0.29246584069654 1.2260789051017942 chr13 115169878 27348450 0.23746183008025762 0.9908485758926633 chr14 107349540 26420843 0.24611975980521203 1.0959863015961282 chr15 102531392 24347587 0.2374647073941998 1.002208808745031 chr16 90354753 24005407 0.2656795154982052 1.1732239678616783 chr17 81195210 22369969 0.2755084813500698 1.3521536500338016 chr18 78077248 23085748 0.2956783005466586 3.913438188023775 chr19 59128983 16199242 0.27396449555034624 2.5971343156673865 chr20 63025520 18051735 0.2864194535800736 1.2445497484721084 chr21 48129895 11164980 0.2319759891435458 1.2879922774132317 chr22 51304566 9692662 0.18892396438944636 0.8916040447623896 chrMT 16571 215453 13.00181039164806 9.921397668610181 chrX 155270560 51539979 0.3319365821827396 1.408586890069711 chrY 59373566 2835360 0.047754584927575346 1.2261056487591315