BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234041.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 = 2,633,666 number of mapped reads = 2,450,712 (93.05%) number of supplementary alignments = 19,954 (0.76%) number of secondary alignments = 0 number of mapped bases = 164,263,861 bp number of sequenced bases = 164,189,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,411 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1624 >>>>>>> ACTG content number of A's = 44,783,724 bp (27.28%) number of C's = 31,447,130 bp (19.15%) number of T's = 50,481,214 bp (30.75%) number of G's = 37,414,665 bp (22.79%) number of N's = 62,382 bp (0.04%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,240,052 number of insertions = 12,713 mapped reads with insertion percentage = 0.51% number of deletions = 41,493 mapped reads with deletion percentage = 1.67% homopolymer indels = 44.46% >>>>>>> Coverage mean coverageData = 0.0531X std coverageData = 0.7042X There is a 4.53% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17986725 0.07216321037771858 1.6811930074048365 chr2 243199373 9341325 0.03841015248012173 0.7019656422158032 chr3 198022430 17745120 0.08961166671876514 0.3388180885659372 chr4 191154276 3629269 0.01898607279912483 0.2033101690381456 chr5 180915260 10106917 0.05586547536122713 0.2698583081538136 chr6 171115067 7686101 0.04491773363242174 0.30943011390811764 chr7 159138663 8143699 0.05117360449358557 0.7551212248564397 chr8 146364022 11168811 0.07630844552768576 0.9939895677724087 chr9 141213431 5088762 0.036035963179734655 0.5089318215985855 chr10 135534747 8239059 0.060789274945117946 0.6381693587959032 chr11 135006516 4562496 0.03379463551225927 0.381146870589054 chr12 133851895 6274254 0.046874599720833236 0.2497625747316924 chr13 115169878 8717637 0.075693724360809 0.31407373365555186 chr14 107349540 11153331 0.10389733388703855 0.41532880760638313 chr15 102531392 3360060 0.03277103660116114 0.2251776914591006 chr16 90354753 4281401 0.04738434734031092 0.3534485326631093 chr17 81195210 4542782 0.05594889156638674 0.2824292673471445 chr18 78077248 3816088 0.048875800540510855 1.3837847382298507 chr19 59128983 4861951 0.08222619015787909 1.0474420566240696 chr20 63025520 3002099 0.047633069905650915 0.28944636193645307 chr21 48129895 3246403 0.06745086395887628 0.3138503484312279 chr22 51304566 1430089 0.0278744975642129 0.18453532829754987 chrMT 16571 114945 6.936515599541368 4.409198244017585 chrX 155270560 5354105 0.034482422166829306 0.2839802081759726 chrY 59373566 410432 0.006912705900130708 0.15008028303964846