BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818826.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 = 1,378,267 number of mapped reads = 1,336,965 (97%) number of supplementary alignments = 11,338 (0.82%) number of secondary alignments = 0 number of mapped bases = 90,901,949 bp number of sequenced bases = 90,863,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 608,468 duplication rate = 37.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8086 >>>>>>> ACTG content number of A's = 24,935,466 bp (27.44%) number of C's = 18,819,403 bp (20.71%) number of T's = 26,808,403 bp (29.5%) number of G's = 20,294,454 bp (22.34%) number of N's = 5,306 bp (0.01%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 458,259 number of insertions = 12,984 mapped reads with insertion percentage = 0.96% number of deletions = 23,611 mapped reads with deletion percentage = 1.75% homopolymer indels = 41.21% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 0.4173X There is a 1.38% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 7516180 0.030155110425983653 0.5392129341976505 chr2 243199373 7831750 0.03220300243126038 0.689138675167371 chr3 198022430 6179315 0.03120512661116218 0.32853300943076175 chr4 191154276 6030499 0.03154781115123995 0.36428865683737444 chr5 180915260 5664812 0.031311963402092226 0.33536495573429675 chr6 171115067 5288678 0.030907143904516602 0.3546974303684119 chr7 159138663 4803883 0.03018677491339738 0.3454687710275716 chr8 146364022 4678178 0.031962622617735935 0.35568540979912555 chr9 141213431 3942428 0.02791822259456326 0.3446031096097065 chr10 135534747 4414153 0.03256842321032259 0.45698853529890243 chr11 135006516 4317693 0.03198136747710755 0.36225946922879926 chr12 133851895 4198606 0.03136754993270734 0.34149758722782786 chr13 115169878 2958518 0.025688296726336726 0.2985898070808489 chr14 107349540 2820918 0.026277876924297953 0.32133733444824114 chr15 102531392 2622044 0.025573084972844218 0.29940378645267035 chr16 90354753 2775166 0.030714111962654583 0.4928414490027294 chr17 81195210 2467296 0.030387211265295082 0.3436983642492806 chr18 78077248 2471167 0.031650283063255506 0.4190954488572284 chr19 59128983 1850048 0.031288344668468256 0.4633132049777756 chr20 63025520 1964778 0.03117432430545595 0.3495401450714884 chr21 48129895 1207752 0.025093593077649558 0.31240146911675 chr22 51304566 1108386 0.02160404202620094 0.29675781382570393 chrMT 16571 192905 11.641120028966267 11.122258494320596 chrX 155270560 2753078 0.01773084350310838 0.26433935301607564 chrY 59373566 843718 0.01421033057034169 0.6629616331282759