BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094156.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 = 29,492 number of mapped reads = 931 (3.16%) number of supplementary alignments = 26 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 333 number of mapped paired reads (second in pair) = 598 number of mapped paired reads (both in pair) = 538 number of mapped paired reads (singletons) = 393 number of mapped bases = 64,499 bp number of sequenced bases = 64,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 657 duplication rate = 26.33% >>>>>>> Insert size mean insert size = 60.8731 std insert size = 49.7707 median insert size = 32 >>>>>>> Mapping quality mean mapping quality = 5.6309 >>>>>>> ACTG content number of A's = 8,580 bp (13.38%) number of C's = 6,355 bp (9.91%) number of T's = 7,049 bp (10.99%) number of G's = 42,163 bp (65.73%) number of N's = 0 bp (0%) GC percentage = 75.64% >>>>>>> Mismatches and indels general error rate = 0.0289 number of mismatches = 1,496 number of insertions = 61 mapped reads with insertion percentage = 5.05% number of deletions = 56 mapped reads with deletion percentage = 5.91% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0471X 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 526 2.110325735156343E-6 0.0017915402413836302 chr2 243199373 37073 1.5243871537448412E-4 0.1574848694504384 chr3 198022430 491 2.479517093088899E-6 0.002106866142224487 chr4 191154276 544 2.8458688520260986E-6 0.002133375201845829 chr5 180915260 718 3.968708886138184E-6 0.002690900102039504 chr6 171115067 896 5.236242580555458E-6 0.003606766261519305 chr7 159138663 1084 6.811669644352862E-6 0.007953173398508501 chr8 146364022 133 9.086932579647203E-7 0.0011718734920742311 chr9 141213431 338 2.393540030905417E-6 0.0020266357127428614 chr10 135534747 137 1.0108109029782598E-6 0.001205612204505833 chr11 135006516 311 2.3035925169715513E-6 0.0016352185496510939 chr12 133851895 356 2.6596560325126513E-6 0.001831514887260569 chr13 115169878 361 3.1345001511593163E-6 0.0021552965023547434 chr14 107349540 261 2.431309905939047E-6 0.0023143742507851827 chr15 102531392 485 4.730258611918582E-6 0.002997097334426887 chr16 90354753 522 5.777227900783482E-6 0.002869525528893549 chr17 81195210 1484 1.8276940228370613E-5 0.006903811420768795 chr18 78077248 247 3.1635336327427936E-6 0.002487201468385999 chr19 59128983 346 5.851614258273308E-6 0.003082954894791748 chr20 63025520 127 2.0150567579609023E-6 0.0014195255184416956 chr21 48129895 217 4.50863231677526E-6 0.0024162672121584954 chr22 51304566 30 5.847432760663057E-7 7.646848593646972E-4 chrMT 16571 298 0.017983223704061312 0.1433752210326693 chrX 155270560 17310 1.114828206969821E-4 0.07252603293103756 chrY 59373566 204 3.435872455429071E-6 0.002100649030257489