BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084994.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 = 3,269,883 number of mapped reads = 3,031,986 (92.72%) number of supplementary alignments = 30,134 (0.92%) number of secondary alignments = 0 number of mapped bases = 208,677,358 bp number of sequenced bases = 208,596,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,066 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0735 >>>>>>> ACTG content number of A's = 60,707,723 bp (29.1%) number of C's = 38,902,957 bp (18.65%) number of T's = 65,562,218 bp (31.43%) number of G's = 43,393,986 bp (20.8%) number of N's = 29,423 bp (0.01%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,713,986 number of insertions = 17,153 mapped reads with insertion percentage = 0.56% number of deletions = 49,266 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.0674X std coverageData = 0.5834X There is a 5.44% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14324758 0.057471303150735176 1.031819493503081 chr2 243199373 19494363 0.08015794925589713 0.6045507881253953 chr3 198022430 14502081 0.07323453711784064 0.326197770340754 chr4 191154276 15156263 0.07928811908973461 0.3509410557750233 chr5 180915260 13530334 0.07478824063818608 0.32492770132459076 chr6 171115067 13357484 0.07806141349317883 0.4660379416439017 chr7 159138663 9723823 0.0611028320628784 0.43535771956033864 chr8 146364022 10175215 0.06951991931459768 1.2619987227991265 chr9 141213431 8895660 0.06299443287373989 0.5338482286855658 chr10 135534747 13489935 0.09953119254356228 0.6662518438267296 chr11 135006516 8558911 0.06339628081358681 0.45306309684410667 chr12 133851895 9560910 0.07142902235340037 0.32453504362139723 chr13 115169878 7102274 0.06166780866087224 0.2915520629644679 chr14 107349540 5930099 0.055241028513023906 0.315548595460417 chr15 102531392 6005949 0.05857668449483257 0.2852765198073837 chr16 90354753 5344678 0.05915215107721007 0.3648417895934328 chr17 81195210 4387646 0.05403823698466942 0.34368638069363555 chr18 78077248 5718309 0.07323912082557008 0.9813490537407981 chr19 59128983 3433636 0.05807026987086857 0.7055172838098636 chr20 63025520 3849400 0.061076846331454306 0.3099328865324331 chr21 48129895 2267889 0.04712017343898216 0.2899054383944912 chr22 51304566 1524146 0.02970780417477852 0.20121358943382198 chrMT 16571 48049 2.8995836099209464 2.34287547978186 chrX 155270560 11795512 0.07596747252022534 0.3881242112250459 chrY 59373566 500034 0.008421828663617745 0.16369367620858807