BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818940.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,117,675 number of mapped reads = 1,100,612 (98.47%) number of supplementary alignments = 14,013 (1.25%) number of secondary alignments = 0 number of mapped bases = 101,997,169 bp number of sequenced bases = 101,942,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 374,768 duplication rate = 27.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2367 >>>>>>> ACTG content number of A's = 29,887,675 bp (29.32%) number of C's = 21,465,176 bp (21.06%) number of T's = 28,702,290 bp (28.16%) number of G's = 21,883,181 bp (21.47%) number of N's = 4,073 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 652,765 number of insertions = 12,222 mapped reads with insertion percentage = 1.08% number of deletions = 31,091 mapped reads with deletion percentage = 2.77% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.4019X There is a 1.89% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 11837395 0.04749193784355707 0.6604543390350335 chr2 243199373 8796004 0.03616787285056035 0.5186414735528052 chr3 198022430 6629748 0.03347978307305895 0.2968370979814793 chr4 191154276 6779071 0.03546387317017172 0.32582585347750415 chr5 180915260 5274109 0.029152372221116118 0.28091951247419433 chr6 171115067 5361250 0.03133125617745865 0.305944164730813 chr7 159138663 5229620 0.032862033030904625 0.3668430825131843 chr8 146364022 6587548 0.045007973339240434 0.38467521035253976 chr9 141213431 3827595 0.0271050350727616 0.4688814378379066 chr10 135534747 4979732 0.036741367879633106 0.47032874790501045 chr11 135006516 3840879 0.028449582389045578 0.3008684566473635 chr12 133851895 4600916 0.03437318537776398 0.30821790550738376 chr13 115169878 1639090 0.01423193311014882 0.19345016312550142 chr14 107349540 3309378 0.030828059440217444 0.2951900169446702 chr15 102531392 3023059 0.029484228596057684 0.280115524092598 chr16 90354753 2950040 0.032649527579362646 0.37157564780296026 chr17 81195210 2144197 0.02640792480246064 0.2796035488120963 chr18 78077248 2617642 0.03352630973878588 0.5908107460573783 chr19 59128983 1483721 0.02509295652861136 0.5721491168408178 chr20 63025520 2200457 0.034913746050806084 0.3148128455792653 chr21 48129895 1360288 0.028262849939730807 0.2923954547086668 chr22 51304566 1200882 0.023406922494968577 0.2593339258906732 chrMT 16571 64040 3.864582704725122 3.805218234347961 chrX 155270560 5980258 0.038515079742096635 0.3907066736688465 chrY 59373566 280250 0.004720113998205868 0.24440668219946812