BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717000.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 4,997,524 number of mapped reads = 4,624,518 (92.54%) number of supplementary alignments = 19,766 (0.4%) number of secondary alignments = 0 number of mapped bases = 270,787,695 bp number of sequenced bases = 270,717,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,167 duplication rate = 5.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8981 >>>>>>> ACTG content number of A's = 68,878,419 bp (25.44%) number of C's = 55,019,177 bp (20.32%) number of T's = 81,873,191 bp (30.24%) number of G's = 64,942,203 bp (23.99%) number of N's = 4,152 bp (0%) GC percentage = 44.31% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,430,640 number of insertions = 17,710 mapped reads with insertion percentage = 0.38% number of deletions = 42,617 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.2% >>>>>>> Coverage mean coverageData = 0.0875X std coverageData = 0.6877X There is a 6.72% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 19356595 0.07765916458840036 1.2638828951636287 chr2 243199373 22642751 0.09310365697365511 0.7673014534181987 chr3 198022430 16346271 0.08254757301988466 0.3516772233727942 chr4 191154276 16544359 0.0865497719758045 0.4529325412354476 chr5 180915260 14904350 0.08238304496812486 0.36282416719042104 chr6 171115067 14117947 0.08250557503507275 0.4321907496970679 chr7 159138663 17273621 0.10854446477283776 0.9631648199468531 chr8 146364022 11824478 0.08078814614700873 0.7495194684548189 chr9 141213431 12637260 0.08949049612709997 0.7144059000567716 chr10 135534747 10215093 0.07536881298786059 0.6452242463498297 chr11 135006516 10443622 0.07735642922597899 0.5678176290833911 chr12 133851895 19994204 0.14937557664013648 0.5996387789444777 chr13 115169878 10203406 0.08859439792060907 0.3717232626010396 chr14 107349540 9542256 0.0888895844360395 0.44136445529200324 chr15 102531392 6933095 0.06761924191958693 0.322209171745317 chr16 90354753 7707510 0.0853027621026201 0.4192851504033274 chr17 81195210 8154208 0.10042720500384197 0.43163737601016705 chr18 78077248 8545916 0.10945462626961443 1.3978458907972866 chr19 59128983 4562179 0.07715639215374294 0.9404186738280703 chr20 63025520 8120613 0.12884642601917445 0.4696836800039536 chr21 48129895 3255855 0.06764724917849914 0.39719092240396947 chr22 51304566 2728990 0.053191951765072916 0.27747073002790323 chrMT 16571 24703 1.4907368294007604 1.5942482606430477 chrX 155270560 13987996 0.09008788272548254 0.5015357488887117 chrY 59373566 720417 0.012133631993739437 0.25783206883404786