BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231792.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 = 3,575,337 number of mapped reads = 2,981,530 (83.39%) number of supplementary alignments = 29,083 (0.81%) number of secondary alignments = 0 number of mapped bases = 186,730,548 bp number of sequenced bases = 186,646,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 771,574 duplication rate = 17.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1382 >>>>>>> ACTG content number of A's = 47,125,535 bp (25.25%) number of C's = 33,409,495 bp (17.9%) number of T's = 61,670,872 bp (33.04%) number of G's = 44,371,626 bp (23.77%) number of N's = 68,496 bp (0.04%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,275,145 number of insertions = 11,909 mapped reads with insertion percentage = 0.4% number of deletions = 52,467 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 0.0603X std coverageData = 0.9286X There is a 2.73% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 49615427 0.1990583887050777 0.9994532195249245 chr2 243199373 5437380 0.022357705667275712 1.5913092262441504 chr3 198022430 12909426 0.06519173610787424 0.5088322582752535 chr4 191154276 7051260 0.03688779632635578 0.35774929047985937 chr5 180915260 3789188 0.020944546081961245 0.2820477684958374 chr6 171115067 4202740 0.024560899713173708 0.8154589745559643 chr7 159138663 10097010 0.06344787501450858 0.5842008185808927 chr8 146364022 33484392 0.22877474629660013 1.541477997194677 chr9 141213431 3411387 0.02415766670239745 0.3113452453478959 chr10 135534747 2935168 0.021656203039948124 0.3682872536425663 chr11 135006516 20340244 0.15066120216004983 0.7511183752602283 chr12 133851895 2023987 0.01512109335471119 0.23391067402387516 chr13 115169878 2243623 0.019480987902062378 0.6362170168523928 chr14 107349540 6023148 0.05610781378290024 0.46316075119783995 chr15 102531392 1820435 0.017754903785954648 0.31688380529863475 chr16 90354753 1842544 0.020392330661343293 0.2954178531194975 chr17 81195210 2198024 0.027070857997657745 0.304631232868548 chr18 78077248 2239847 0.028687576180963754 2.9963946721572077 chr19 59128983 1759037 0.02974915026020319 0.41865968074126847 chr20 63025520 1357525 0.02153929075079428 0.2734688770294465 chr21 48129895 1386503 0.02880752181154769 0.3098678074793308 chr22 51304566 505875 0.00986023349266808 0.17096064235894276 chrMT 16571 1592522 96.10295093838634 63.31208390065127 chrX 155270560 8119630 0.05229342896683054 0.4352011573418468 chrY 59373566 344226 0.005797630548247683 0.25950864765765236