BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063526.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 = 5,037,811 number of mapped reads = 4,763,398 (94.55%) number of supplementary alignments = 39,722 (0.79%) number of secondary alignments = 0 number of mapped bases = 305,517,386 bp number of sequenced bases = 305,383,048 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 704,760 duplication rate = 12.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8574 >>>>>>> ACTG content number of A's = 79,094,490 bp (25.9%) number of C's = 55,070,841 bp (18.03%) number of T's = 99,269,256 bp (32.51%) number of G's = 71,913,470 bp (23.55%) number of N's = 34,991 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,672,413 number of insertions = 19,042 mapped reads with insertion percentage = 0.4% number of deletions = 76,744 mapped reads with deletion percentage = 1.6% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.0987X std coverageData = 1.1472X There is a 6.8% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 31322177 0.12566539202323593 2.537810277144092 chr2 243199373 36423926 0.14976981869110328 1.689255994405297 chr3 198022430 20543915 0.10374539389300495 0.43958022049143997 chr4 191154276 16843204 0.08811314270573785 0.45050906224042087 chr5 180915260 16482539 0.09110640528609913 0.4174810407428965 chr6 171115067 22620990 0.13219753465660625 0.6927582885234428 chr7 159138663 25226198 0.15851709147512444 2.151073747141495 chr8 146364022 9672202 0.06608319358701416 0.9557398938296326 chr9 141213431 11114291 0.07870562255512367 0.7020478390868614 chr10 135534747 13838458 0.1021026585898301 0.7373908915309425 chr11 135006516 11512224 0.0852716175565926 0.5272991150341112 chr12 133851895 12030957 0.08988260494929863 0.45511334047511554 chr13 115169878 7807677 0.06779270010167068 0.404847920888264 chr14 107349540 1767345 0.01646346132456646 0.3255381180357831 chr15 102531392 7194822 0.07017189428189954 0.4113123390858092 chr16 90354753 8052359 0.08911937372016279 0.4706601601391948 chr17 81195210 7664218 0.09439248940916589 0.46084390996102936 chr18 78077248 9116662 0.11676464313906146 1.3810473051736087 chr19 59128983 6797666 0.11496335054502797 1.7059511957542517 chr20 63025520 3638975 0.05773811941575412 0.3750067717904097 chr21 48129895 5253452 0.10915153669044987 0.4921188906417217 chr22 51304566 2439343 0.04754631390898034 0.2888463469699945 chrMT 16571 398144 24.02655241083821 13.093781289572565 chrX 155270560 16943181 0.10912037027495747 0.5462198387337835 chrY 59373566 812461 0.013683884171619403 0.4587172873347847