BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054575.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 = 9,798,840 number of mapped reads = 6,896,583 (70.38%) number of supplementary alignments = 197 (0%) number of secondary alignments = 0 number of mapped bases = 326,275,486 bp number of sequenced bases = 326,208,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,877,550 duplication rate = 21.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3226 >>>>>>> ACTG content number of A's = 94,752,249 bp (29.05%) number of C's = 64,048,925 bp (19.63%) number of T's = 96,489,310 bp (29.58%) number of G's = 70,703,858 bp (21.67%) number of N's = 214,324 bp (0.07%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,985,723 number of insertions = 13,741 mapped reads with insertion percentage = 0.2% number of deletions = 44,738 mapped reads with deletion percentage = 0.65% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.1054X std coverageData = 0.8483X There is a 4.25% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% 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 0.02% 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% 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 29628854 0.11887173593039915 0.944053445672975 chr2 243199373 31891222 0.13113200748260154 1.1364549779920163 chr3 198022430 22146867 0.1118401940628645 0.8013985524190647 chr4 191154276 15591060 0.08156270592659931 0.6775915701080413 chr5 180915260 18153851 0.10034449830268602 0.7472271495759842 chr6 171115067 19879925 0.11617869395451892 0.8836528845056278 chr7 159138663 16942549 0.10646406524101563 0.9284534364499359 chr8 146364022 17991450 0.12292262643616066 0.8889737999083668 chr9 141213431 17035221 0.12063456626870003 0.8820354944163074 chr10 135534747 11241794 0.08294399959296046 0.7394952535906114 chr11 135006516 14209482 0.10525034213904165 0.8376236659963205 chr12 133851895 17267477 0.12900435216102096 0.8876175738375307 chr13 115169878 8154207 0.07080155976200653 0.6245228972352531 chr14 107349540 6339276 0.059052661054719006 0.6735226532607886 chr15 102531392 8417050 0.08209241907102949 0.6756729578027704 chr16 90354753 8143857 0.09013202659078709 0.7457847805760375 chr17 81195210 7527041 0.09270301782580524 0.7226886563341877 chr18 78077248 11186638 0.1432765406895489 1.0288504658674091 chr19 59128983 7015942 0.11865487353300157 0.9269810899117852 chr20 63025520 7160529 0.11361316812618127 0.8145380476366471 chr21 48129895 3709309 0.0770687116603932 0.699556468034808 chr22 51304566 4806582 0.09368721684537785 0.7570678437081816 chrMT 16571 32875 1.9838875143322672 5.033911920447533 chrX 155270560 21030901 0.13544680330901107 0.9388845242061279 chrY 59373566 771527 0.01299445278392071 0.2630431477271021