BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008718.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 = 1,947,853 number of mapped reads = 1,487,538 (76.37%) number of supplementary alignments = 7,493 (0.38%) number of secondary alignments = 0 number of mapped bases = 101,878,732 bp number of sequenced bases = 101,832,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,492 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.4939 >>>>>>> ACTG content number of A's = 31,171,511 bp (30.61%) number of C's = 18,092,479 bp (17.77%) number of T's = 30,480,151 bp (29.93%) number of G's = 22,062,265 bp (21.67%) number of N's = 26,512 bp (0.03%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 898,503 number of insertions = 7,002 mapped reads with insertion percentage = 0.47% number of deletions = 27,587 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.2558X There is a 2.94% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 8349365 0.03349787040249741 0.3962393946071573 chr2 243199373 9225543 0.03793407395010019 0.29994612822939243 chr3 198022430 8367588 0.04225575860269971 0.2258710150423463 chr4 191154276 6075697 0.03178425890928017 0.19644284132054052 chr5 180915260 4983456 0.027545802382839348 0.18029383603936644 chr6 171115067 5561459 0.03250128172523814 0.21159428040369632 chr7 159138663 5678940 0.03568548266614506 0.30582933866979484 chr8 146364022 8818193 0.06024836486114053 0.38244758961807396 chr9 141213431 3085430 0.021849408927681956 0.2047562992450588 chr10 135534747 5108982 0.03769499787386625 0.25052602783213684 chr11 135006516 4601645 0.03408461410855162 0.2573412517588796 chr12 133851895 4636807 0.03464132502569351 0.20300580564305432 chr13 115169878 3049008 0.026474005642343392 0.1764596979941551 chr14 107349540 3193877 0.02975212562624861 0.1948092095329492 chr15 102531392 2470448 0.024094552427416573 0.16936022160243316 chr16 90354753 2462724 0.02725616437687567 0.1925411827494516 chr17 81195210 2715034 0.033438351843661715 0.2196249380952918 chr18 78077248 1915223 0.02452984767086053 0.3705421430841554 chr19 59128983 1575333 0.026642315157018683 0.23404993129790988 chr20 63025520 2363533 0.03750120586073705 0.21367284448398574 chr21 48129895 1120653 0.02328392779581173 0.17113668002561394 chr22 51304566 1063132 0.020721976285697455 0.1562313350871122 chrMT 16571 28231 1.7036388872126003 2.0729009299389793 chrX 155270560 5225882 0.03365661848582242 0.2166230684419177 chrY 59373566 202549 0.00341143397046423 0.08113590623289867