BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234102.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,093,414 number of mapped reads = 4,814,782 (94.53%) number of supplementary alignments = 44,332 (0.87%) number of secondary alignments = 0 number of mapped bases = 308,932,579 bp number of sequenced bases = 308,805,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 653,927 duplication rate = 11.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.8772 >>>>>>> ACTG content number of A's = 80,447,404 bp (26.05%) number of C's = 55,818,208 bp (18.08%) number of T's = 100,695,363 bp (32.61%) number of G's = 71,814,716 bp (23.26%) number of N's = 30,303 bp (0.01%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,575,165 number of insertions = 18,285 mapped reads with insertion percentage = 0.38% number of deletions = 72,667 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.0998X std coverageData = 0.754X There is a 7.05% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 10521372 0.04221201920295316 0.6997694624035341 chr2 243199373 12064925 0.049609194510546704 1.4847704618146487 chr3 198022430 35702682 0.18029615129962803 0.555747730260103 chr4 191154276 1973997 0.010326721647597358 0.24605568250884777 chr5 180915260 34728479 0.19195992090440575 0.5755958545597728 chr6 171115067 37530597 0.21932958714851217 0.9342080874937734 chr7 159138663 32873061 0.2065686639581734 1.4233503175624431 chr8 146364022 19509715 0.1332958382354374 0.612082384620843 chr9 141213431 15237476 0.10790387211822648 0.4754394731955495 chr10 135534747 16807317 0.12400743995191137 0.7781574769128012 chr11 135006516 13534442 0.10025028717873143 0.60345321352022 chr12 133851895 1256500 0.00938724102486558 0.1877865740002083 chr13 115169878 1938138 0.01682851483093522 0.26861842425416715 chr14 107349540 15760676 0.1468164279045816 0.5021132179211717 chr15 102531392 6363537 0.06206427978662379 0.36945200740724904 chr16 90354753 10442782 0.11557534776283435 0.4595646934147142 chr17 81195210 3089900 0.03805520054692881 0.3137688321618243 chr18 78077248 830435 0.010636069037679196 0.7586166414014539 chr19 59128983 6119986 0.10350230444518216 0.8853663658029431 chr20 63025520 1851775 0.02938135218876417 0.2507667058428576 chr21 48129895 5626586 0.11690418190191357 0.4673686891076602 chr22 51304566 340757 0.0066418454840842045 0.10168814610788134 chrMT 16571 476971 28.78347715889204 15.34003790664151 chrX 155270560 23564969 0.15176714117602202 0.5951367498981563 chrY 59373566 785504 0.01322986057465371 0.2734496416818014