BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084387.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,838,353 number of mapped reads = 1,688,289 (91.84%) number of supplementary alignments = 10,120 (0.55%) number of secondary alignments = 0 number of mapped bases = 113,054,876 bp number of sequenced bases = 113,014,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,398 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.313 >>>>>>> ACTG content number of A's = 31,465,404 bp (27.84%) number of C's = 21,170,282 bp (18.73%) number of T's = 35,195,127 bp (31.14%) number of G's = 25,037,789 bp (22.15%) number of N's = 145,732 bp (0.13%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,106,265 number of insertions = 7,982 mapped reads with insertion percentage = 0.47% number of deletions = 23,234 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.3004X There is a 3.25% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 11266389 0.04520104686118315 0.538918476590274 chr2 243199373 10948336 0.0450179450092579 0.317460817830192 chr3 198022430 7674086 0.03875361998133242 0.22203678287022346 chr4 191154276 5460433 0.028565581237638648 0.19200917204272544 chr5 180915260 5754242 0.03180628322895482 0.1937356200348557 chr6 171115067 5392524 0.031514022081994685 0.21596421809040092 chr7 159138663 6490397 0.04078453895267425 0.445198213632316 chr8 146364022 5669338 0.03873450539641497 0.27895432613928905 chr9 141213431 4209278 0.029807915367483707 0.24329114931985546 chr10 135534747 8156296 0.060178634486992476 0.4562649358025019 chr11 135006516 6428683 0.047617575732418725 0.28401931302104344 chr12 133851895 4109955 0.03070524328400431 0.19214475856298205 chr13 115169878 3035220 0.026354286838786094 0.17593096608329187 chr14 107349540 3096692 0.028846812012422222 0.19014948465259943 chr15 102531392 2579321 0.025156402831242163 0.18002101874503332 chr16 90354753 2494917 0.02761245996654985 0.20167151708940573 chr17 81195210 3150901 0.03880648870789299 0.22536745901521876 chr18 78077248 3010885 0.03856289863085338 0.4000685133026068 chr19 59128983 2313438 0.03912527972957018 0.36281342477203116 chr20 63025520 2280908 0.03619022897391406 0.2099938949795068 chr21 48129895 1177456 0.024464129830326867 0.1789401505688464 chr22 51304566 955133 0.01861691998330129 0.14776385211840812 chrMT 16571 10069 0.6076277834771588 0.8180273709879786 chrX 155270560 7137254 0.04596656313985085 0.2585053868141309 chrY 59373566 252725 0.00425652385440349 0.09611773552073424