BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081099.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 = 2,612,093 number of mapped reads = 2,398,596 (91.83%) number of supplementary alignments = 21,599 (0.83%) number of secondary alignments = 0 number of mapped bases = 161,876,963 bp number of sequenced bases = 161,818,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,433 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.686 >>>>>>> ACTG content number of A's = 44,814,790 bp (27.69%) number of C's = 30,260,544 bp (18.7%) number of T's = 50,726,395 bp (31.35%) number of G's = 36,015,423 bp (22.26%) number of N's = 1,757 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,484,249 number of insertions = 12,626 mapped reads with insertion percentage = 0.52% number of deletions = 35,718 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.5931X There is a 4.47% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13761115 0.055209952716627334 1.1514051485882055 chr2 243199373 11083369 0.045573180815725214 0.5916530164734642 chr3 198022430 13408511 0.06771208190910494 0.3010817395939422 chr4 191154276 9734798 0.050926394134128604 0.27151956858880494 chr5 180915260 8722438 0.04821283732505483 0.2580001454324972 chr6 171115067 13488113 0.07882481207806206 0.7317907948094085 chr7 159138663 8359041 0.05252677660110793 0.6908210475864536 chr8 146364022 11700724 0.07994262415117288 0.5874668876264235 chr9 141213431 8386621 0.05938968369092314 0.6956961733931607 chr10 135534747 7517743 0.0554672743809379 0.5550515544545502 chr11 135006516 7065405 0.052333807354898336 0.44602155428370743 chr12 133851895 8007064 0.059820326040210335 0.3121430450577886 chr13 115169878 4160153 0.03612188423087502 0.2114354948550598 chr14 107349540 4645823 0.0432775305790784 0.3661149386328869 chr15 102531392 4363077 0.042553572275698746 0.23281213934088704 chr16 90354753 3847565 0.04258287331049425 0.39542390190171245 chr17 81195210 3481809 0.042881950794880636 0.2640323522146481 chr18 78077248 4378767 0.05608249665766908 1.3758985915787365 chr19 59128983 3121459 0.052790676274611384 0.818394249154173 chr20 63025520 2629413 0.041719814449765746 0.27189003434624354 chr21 48129895 3734825 0.07759886033410213 0.3845293396930412 chr22 51304566 1400724 0.027302131354156666 0.1827929839656531 chrMT 16571 81454 4.915454710035604 3.3030265732435824 chrX 155270560 4400175 0.028338759131157895 0.28175147007110835 chrY 59373566 396777 0.006682721398273433 0.17132241973324713