BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230381.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 = 2,492,068 number of mapped reads = 1,889,955 (75.84%) number of supplementary alignments = 14,378 (0.58%) number of secondary alignments = 0 number of mapped bases = 124,070,945 bp number of sequenced bases = 124,019,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,181 duplication rate = 5.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2504 >>>>>>> ACTG content number of A's = 33,821,543 bp (27.27%) number of C's = 21,453,701 bp (17.3%) number of T's = 41,826,920 bp (33.73%) number of G's = 26,680,541 bp (21.51%) number of N's = 236,803 bp (0.19%) GC percentage = 38.81% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,298,744 number of insertions = 10,305 mapped reads with insertion percentage = 0.54% number of deletions = 32,043 mapped reads with deletion percentage = 1.68% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.3404X There is a 3.02% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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% 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 15187911 0.060934295525787274 0.5470133457270302 chr2 243199373 3813245 0.01567950177239972 0.2912976226922048 chr3 198022430 11204595 0.05658245381596418 0.3028157850514202 chr4 191154276 10237070 0.05355396810479929 0.2936632876691898 chr5 180915260 1966608 0.0108703268038307 0.12653353787414862 chr6 171115067 19689192 0.11506404634724539 0.5907537008873733 chr7 159138663 2146446 0.013487897658157402 0.20934807608126413 chr8 146364022 7770880 0.05309282905603674 0.49178637734777775 chr9 141213431 1255487 0.008890705304086833 0.21200540863525846 chr10 135534747 2228047 0.016438935766043817 0.3400105992727723 chr11 135006516 3584233 0.02654859266200159 0.2395899279656941 chr12 133851895 5252143 0.03923846576845251 0.2539033719393494 chr13 115169878 1629057 0.01414481831785912 0.14776530277362115 chr14 107349540 5370615 0.050029231611053014 0.2881527968076391 chr15 102531392 4446742 0.04336956626903105 0.2623735406275 chr16 90354753 5733828 0.06345906340975775 0.3346142768750023 chr17 81195210 3891102 0.047922802342650506 0.28284372960970544 chr18 78077248 4157452 0.05324793209924612 0.438367433594949 chr19 59128983 544453 0.009207887103351667 0.3473168291042023 chr20 63025520 2213863 0.0351264535381858 0.23771659592100094 chr21 48129895 433750 0.009012070356687876 0.11983748973305679 chr22 51304566 427827 0.008338965385653978 0.10854756911815977 chrMT 16571 56542 3.4121054854866935 2.7738577677860525 chrX 155270560 10546772 0.0679251237324062 0.3609629605925602 chrY 59373566 283085 0.004767862519829111 0.08993211407878055