BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237577.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 = 2,122,646 number of mapped reads = 1,619,197 (76.28%) number of supplementary alignments = 7,878 (0.37%) number of secondary alignments = 0 number of mapped bases = 98,259,191 bp number of sequenced bases = 98,208,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,977 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3338 >>>>>>> ACTG content number of A's = 26,006,712 bp (26.48%) number of C's = 18,846,208 bp (19.19%) number of T's = 28,606,173 bp (29.13%) number of G's = 24,581,921 bp (25.03%) number of N's = 167,088 bp (0.17%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 957,800 number of insertions = 8,895 mapped reads with insertion percentage = 0.54% number of deletions = 30,793 mapped reads with deletion percentage = 1.88% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.2817X There is a 2.61% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 8177607 0.03280877282147273 0.31909652570733726 chr2 243199373 8363443 0.034389245732142575 0.38589134798505503 chr3 198022430 6363800 0.03213676349694325 0.2293384814418265 chr4 191154276 6079492 0.03180411198334899 0.24060094934535833 chr5 180915260 5181855 0.02864244287629468 0.2086393346964138 chr6 171115067 5646758 0.032999770850102875 0.24813661810242735 chr7 159138663 5799318 0.03644191732338483 0.3894609405149707 chr8 146364022 5544113 0.037878933116500445 0.293655640073879 chr9 141213431 4095454 0.029001873058377852 0.30862822191041983 chr10 135534747 4502656 0.03322141443182832 0.284200404805208 chr11 135006516 4073562 0.030173076979484455 0.27489505543686926 chr12 133851895 5803978 0.04336119410188403 0.2735383244646819 chr13 115169878 3322524 0.028848897452161928 0.21517632524680333 chr14 107349540 2810706 0.026182748430966726 0.2269355414902468 chr15 102531392 2971709 0.028983406369826718 0.2206858581579534 chr16 90354753 2615351 0.02894536162364364 0.24397434270816487 chr17 81195210 2373151 0.029227721684567352 0.22427083590451727 chr18 78077248 2443750 0.03129913083002106 0.41150527230535955 chr19 59128983 1943714 0.0328724409144666 0.2857707045299311 chr20 63025520 2133408 0.03384990714872325 0.23680880988673758 chr21 48129895 1206203 0.025061409338208614 0.21546319268887762 chr22 51304566 1037560 0.02022354111717854 0.18329515045076106 chrMT 16571 90493 5.460925713596041 4.659017065637599 chrX 155270560 5332710 0.034344630430907186 0.2512570072737879 chrY 59373566 345876 0.005825420693107771 0.14380009954946382