BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004145.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 = 4,130,397 number of mapped reads = 3,535,259 (85.59%) number of supplementary alignments = 28,368 (0.69%) number of secondary alignments = 0 number of mapped bases = 236,263,030 bp number of sequenced bases = 236,157,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 365,335 duplication rate = 8.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.151 >>>>>>> ACTG content number of A's = 66,618,560 bp (28.21%) number of C's = 41,822,736 bp (17.71%) number of T's = 77,972,148 bp (33.02%) number of G's = 49,717,456 bp (21.05%) number of N's = 26,351 bp (0.01%) GC percentage = 38.76% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 2,140,683 number of insertions = 19,455 mapped reads with insertion percentage = 0.55% number of deletions = 63,938 mapped reads with deletion percentage = 1.79% homopolymer indels = 48.44% >>>>>>> Coverage mean coverageData = 0.0763X std coverageData = 0.6341X There is a 4.38% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 14047966 0.0563608064190139 0.657634953876113 chr2 243199373 28352099 0.11657965499771251 0.7039611712375279 chr3 198022430 10174250 0.05137928061987725 0.358421538205813 chr4 191154276 25635019 0.13410643767131844 0.582748439981057 chr5 180915260 16125950 0.08913537752426191 0.4660381779222271 chr6 171115067 15824430 0.09247829707479821 0.5169805947231908 chr7 159138663 19684033 0.12369107939533211 0.6265361201397007 chr8 146364022 19542501 0.1335198413719459 1.5381026210100008 chr9 141213431 3768314 0.02668523789355419 0.35634548011646316 chr10 135534747 4526460 0.033397044670766235 0.40123370937493874 chr11 135006516 19579023 0.1450228002328421 1.0962716259953844 chr12 133851895 4014280 0.029990460725266534 0.2781277643809552 chr13 115169878 14673916 0.12741105795041305 0.5505683252586969 chr14 107349540 5854396 0.05453582754057446 0.37718269113016145 chr15 102531392 2387752 0.023288009198197564 0.24754078041086883 chr16 90354753 3565536 0.039461521188597574 0.32018310097406594 chr17 81195210 2322202 0.028600233930055726 0.42445167144794355 chr18 78077248 10332977 0.1323429970277641 0.8275697029569198 chr19 59128983 2510198 0.042452920254014856 0.47429254326780806 chr20 63025520 2205408 0.03499230153118927 0.3048946649421013 chr21 48129895 4047823 0.0841020534119179 0.47772203176354744 chr22 51304566 1360342 0.026515027921686345 0.2477173841044623 chrMT 16571 574796 34.686862591273915 21.301400031741505 chrX 155270560 4783644 0.030808441729069568 0.341927881825389 chrY 59373566 369715 0.006226929337543916 0.1634186766667827