BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472420.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 33,776,426 number of mapped reads = 33,419,478 (98.94%) number of supplementary alignments = 50,334 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,812,746 number of mapped paired reads (second in pair) = 16,606,732 number of mapped paired reads (both in pair) = 33,166,630 number of mapped paired reads (singletons) = 252,848 number of mapped bases = 3,284,973,407 bp number of sequenced bases = 3,284,506,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,397,781 duplication rate = 52.95% >>>>>>> Insert size mean insert size = 34,679.8942 std insert size = 1,872,161.0338 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 54.8705 >>>>>>> ACTG content number of A's = 919,876,504 bp (28.01%) number of C's = 722,658,891 bp (22%) number of T's = 924,871,630 bp (28.16%) number of G's = 716,650,055 bp (21.82%) number of N's = 449,561 bp (0.01%) GC percentage = 43.82% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 15,964,862 number of insertions = 159,047 mapped reads with insertion percentage = 0.47% number of deletions = 195,999 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 1.0611X std coverageData = 20.1436X There is a 8.62% of reference with a coverageData >= 1X There is a 3.58% of reference with a coverageData >= 2X There is a 1.41% of reference with a coverageData >= 3X There is a 1.04% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.66% of reference with a coverageData >= 7X There is a 0.64% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.57% of reference with a coverageData >= 12X There is a 0.56% of reference with a coverageData >= 13X There is a 0.55% of reference with a coverageData >= 14X There is a 0.54% of reference with a coverageData >= 15X There is a 0.53% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.51% of reference with a coverageData >= 18X There is a 0.51% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.49% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.48% of reference with a coverageData >= 23X There is a 0.47% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.46% of reference with a coverageData >= 26X There is a 0.46% of reference with a coverageData >= 27X There is a 0.45% of reference with a coverageData >= 28X There is a 0.45% of reference with a coverageData >= 29X There is a 0.44% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.43% of reference with a coverageData >= 32X There is a 0.43% of reference with a coverageData >= 33X There is a 0.42% of reference with a coverageData >= 34X There is a 0.42% of reference with a coverageData >= 35X There is a 0.41% of reference with a coverageData >= 36X There is a 0.41% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.4% of reference with a coverageData >= 40X There is a 0.4% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.39% of reference with a coverageData >= 44X There is a 0.38% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.38% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 339432260 1.3618110905328498 23.017099399076596 chr2 243199373 247767003 1.0187814217761162 20.931269881283416 chr3 198022430 281041345 1.4192399568069132 21.701939601021014 chr4 191154276 115657307 0.6050469255524266 14.94528512075098 chr5 180915260 150653914 0.8327319320658744 17.071981474437443 chr6 171115067 232888322 1.361004183226016 21.381172655910625 chr7 159138663 209806741 1.3183894915593202 25.564878286643545 chr8 146364022 181607232 1.240791483579209 21.2794192095025 chr9 141213431 150202621 1.06365676364028 17.532299396496786 chr10 135534747 88934299 0.6561734239264858 14.320377058447844 chr11 135006516 125501971 0.9295993609671402 19.029964787858912 chr12 133851895 147965113 1.1054390600895116 17.690825135666014 chr13 115169878 98568886 0.8558564766387962 21.92008422190453 chr14 107349540 84035691 0.7828230190832676 15.949047267653036 chr15 102531392 80835982 0.7884022680585474 18.28431661906619 chr16 90354753 165906012 1.8361625314829868 31.557705701637865 chr17 81195210 170143122 2.095482258128281 31.156491045764906 chr18 78077248 51247662 0.656371264519979 13.171439437376115 chr19 59128983 84879324 1.4354944004364154 18.978449348087878 chr20 63025520 77505394 1.2297462043946643 22.70353520495762 chr21 48129895 27541276 0.572228050778004 21.530448791130713 chr22 51304566 50887172 0.9918643888343194 20.190047656481166 chrMT 16571 126378 7.626455856616982 3.9014572672200645 chrX 155270560 116169930 0.7481774394321756 11.693424164004599 chrY 59373566 5668450 0.09547093735282802 2.623658886018062