BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714144.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 696,964 number of mapped reads = 592,887 (85.07%) number of supplementary alignments = 16,705 (2.4%) number of secondary alignments = 0 number of mapped bases = 78,048,143 bp number of sequenced bases = 75,969,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 525,193 duplication rate = 44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.8643 >>>>>>> ACTG content number of A's = 21,479,930 bp (28.27%) number of C's = 15,794,837 bp (20.79%) number of T's = 20,448,102 bp (26.92%) number of G's = 18,245,827 bp (24.02%) number of N's = 513 bp (0%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0498 number of mismatches = 3,557,351 number of insertions = 86,548 mapped reads with insertion percentage = 14.07% number of deletions = 319,347 mapped reads with deletion percentage = 49.86% homopolymer indels = 30.34% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 5.1096X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4528181 0.01816718041396575 2.802172578134 chr2 243199373 8180672 0.03363771830118986 9.07672735237225 chr3 198022430 3947035 0.01993226221898196 4.062575178041797 chr4 191154276 3300506 0.01726618974508318 2.988404752711286 chr5 180915260 5180784 0.028636522977663687 5.376990949005073 chr6 171115067 3955480 0.023115907145686943 4.376870501285659 chr7 159138663 3910876 0.024575272446520427 4.172361287736121 chr8 146364022 5139040 0.03511136090534599 8.246547105251029 chr9 141213431 2353009 0.016662784717694452 2.9377495264959372 chr10 135534747 4129018 0.030464645350317437 4.476509438934765 chr11 135006516 4414403 0.03269770327233687 6.354374898893815 chr12 133851895 3209098 0.023974991164674955 4.330512241091955 chr13 115169878 2349114 0.020396947889447275 3.301326158710474 chr14 107349540 3898812 0.036318851482735746 5.991240156804876 chr15 102531392 1821977 0.017769943082407386 1.9170221522300357 chr16 90354753 1713735 0.01896673880564977 2.9037451326980377 chr17 81195210 2561487 0.0315472673819059 8.47054577177713 chr18 78077248 1566111 0.020058481057119226 2.4306671221596843 chr19 59128983 1113854 0.018837699271776753 2.7427862785447115 chr20 63025520 1388574 0.02203193246164411 3.5287163917602213 chr21 48129895 740700 0.015389603488642559 2.428863490606726 chr22 51304566 599917 0.011693247731595663 1.5697739743588406 chrMT 16571 142954 8.626757588558325 64.44444444196084 chrX 155270560 7671864 0.049409649839609 6.446948653943767 chrY 59373566 230942 0.003889643414714218 0.6848284955313096