BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234060.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 = 903,467 number of mapped reads = 100,472 (11.12%) number of supplementary alignments = 1,463 (0.16%) number of secondary alignments = 0 number of mapped bases = 5,771,019 bp number of sequenced bases = 5,768,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,027 duplication rate = 9.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 30.5655 >>>>>>> ACTG content number of A's = 1,506,652 bp (26.12%) number of C's = 1,091,098 bp (18.92%) number of T's = 1,799,996 bp (31.21%) number of G's = 1,369,048 bp (23.74%) number of N's = 1,239 bp (0.02%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 54,456 number of insertions = 1,151 mapped reads with insertion percentage = 1.11% number of deletions = 1,738 mapped reads with deletion percentage = 1.7% homopolymer indels = 33.51% >>>>>>> Coverage mean coverageData = 0.0019X std coverageData = 0.07X There is a 0.13% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.01% 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 725814 0.0029119847207923306 0.08592578718378904 chr2 243199373 343373 0.0014118991992631495 0.0722659086712571 chr3 198022430 364348 0.0018399329813294384 0.06382757124001295 chr4 191154276 259540 0.0013577514739978927 0.05911391261053444 chr5 180915260 238832 0.001320131867262054 0.05823188185112577 chr6 171115067 257315 0.0015037541959995843 0.058699301213058684 chr7 159138663 1249949 0.007854464631263115 0.13235435801841872 chr8 146364022 223493 0.001526966784227889 0.060776510801857475 chr9 141213431 207835 0.0014717792672284834 0.05799966129184461 chr10 135534747 194945 0.0014383396458474225 0.05890628926182694 chr11 135006516 205675 0.0015234449869071505 0.062393115671618184 chr12 133851895 191205 0.001428481830608375 0.05672601827754252 chr13 115169878 136970 0.0011892866640008076 0.09807540071215552 chr14 107349540 135251 0.0012599122455485138 0.06786222003928978 chr15 102531392 112996 0.0011020624785821693 0.05244176950169037 chr16 90354753 135104 0.0014952616825813247 0.06419866199209145 chr17 81195210 129134 0.0015904140158021637 0.06120452600720503 chr18 78077248 111583 0.0014291359244629114 0.06572319297320678 chr19 59128983 87524 0.001480221636824026 0.05726916154178672 chr20 63025520 104379 0.0016561386562141812 0.06346197203166604 chr21 48129895 62538 0.001299358745744199 0.052808546717678075 chr22 51304566 47499 9.258240289957818E-4 0.04173179276485149 chrMT 16571 5774 0.3484400458632551 0.8784737223246989 chrX 155270560 218928 0.001409977525681623 0.05836597922072396 chrY 59373566 21015 3.5394539044530357E-4 0.02839710338339051