BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714101.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 25,220 number of mapped reads = 3,592 (14.24%) number of supplementary alignments = 150 (0.59%) number of secondary alignments = 0 number of mapped bases = 417,217 bp number of sequenced bases = 407,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,383 duplication rate = 39.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 28.4369 >>>>>>> ACTG content number of A's = 105,184 bp (25.8%) number of C's = 73,187 bp (17.95%) number of T's = 98,260 bp (24.11%) number of G's = 130,986 bp (32.13%) number of N's = 3 bp (0%) GC percentage = 50.09% >>>>>>> Mismatches and indels general error rate = 0.0413 number of mismatches = 16,079 number of insertions = 275 mapped reads with insertion percentage = 7.1% number of deletions = 1,372 mapped reads with deletion percentage = 36.8% homopolymer indels = 33.03% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.0749X 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 18408 7.385337667824708E-5 0.03182613783287123 chr2 243199373 81051 3.3326977368481947E-4 0.23376520567375705 chr3 198022430 24918 1.2583422999101667E-4 0.037786273406251444 chr4 191154276 18397 9.624163468883113E-5 0.031582057073598346 chr5 180915260 14672 8.109874202983209E-5 0.028113113402919478 chr6 171115067 17964 1.0498198852354713E-4 0.04187773615849288 chr7 159138663 6997 4.3967945112118986E-5 0.017888954512347708 chr8 146364022 17705 1.2096551979146897E-4 0.03572453629085302 chr9 141213431 8207 5.8117701282960826E-5 0.02068785367467231 chr10 135534747 13957 1.0297728301363193E-4 0.029087763400623613 chr11 135006516 27416 2.0307167988839887E-4 0.05012262170123636 chr12 133851895 9866 7.37083326313759E-5 0.023243409099736535 chr13 115169878 11224 9.745603794075392E-5 0.04627302607614946 chr14 107349540 18155 1.6912042659894023E-4 0.05046668142551659 chr15 102531392 4097 3.995849388253697E-5 0.019762634468362628 chr16 90354753 3801 4.206751580627972E-5 0.02087376718304438 chr17 81195210 5945 7.32186048906087E-5 0.025787776980602254 chr18 78077248 9198 1.1780640629136929E-4 0.03302964394997505 chr19 59128983 2500 4.228044984301523E-5 0.014637000254605691 chr20 63025520 2562 4.0650200109415995E-5 0.011985594358035551 chr21 48129895 1489 3.09371129939095E-5 0.015351674551924975 chr22 51304566 450 8.771149140994586E-6 0.003769507264521276 chrMT 16571 1494 0.0901575040733812 0.8370748840289955 chrX 155270560 95907 6.176766542221526E-4 0.09061355682330388 chrY 59373566 837 1.409718257448104E-5 0.006589370131045783