BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525137.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,953,574 number of mapped reads = 1,787,264 (91.49%) number of supplementary alignments = 7,521 (0.38%) number of secondary alignments = 0 number of mapped bases = 104,025,233 bp number of sequenced bases = 103,997,642 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,922 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9529 >>>>>>> ACTG content number of A's = 26,655,978 bp (25.63%) number of C's = 19,834,372 bp (19.07%) number of T's = 32,790,256 bp (31.53%) number of G's = 24,713,897 bp (23.76%) number of N's = 3,139 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 495,799 number of insertions = 7,056 mapped reads with insertion percentage = 0.39% number of deletions = 16,717 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.3052X There is a 2.96% of reference with a coverageData >= 1X There is a 0.29% 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 0.01% 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 8329964 0.03342003308388949 0.5485902171520715 chr2 243199373 8749912 0.035978349335629246 0.3175992479463322 chr3 198022430 6978149 0.035239184773159286 0.20676321446161688 chr4 191154276 6715796 0.03513285781794387 0.2335746922589677 chr5 180915260 6096681 0.03369909757750673 0.2050528473043278 chr6 171115067 5908036 0.034526684900284085 0.2249719783292077 chr7 159138663 5802259 0.03646039806178339 0.37579124287236404 chr8 146364022 5435041 0.037133722657607754 0.3671707207061579 chr9 141213431 4371183 0.030954442286725545 0.29233643821217004 chr10 135534747 5006987 0.0369424602238716 0.28125565573651823 chr11 135006516 4684204 0.03469613274073379 0.2820077503092784 chr12 133851895 4729550 0.035334202776882616 0.2152459023653441 chr13 115169878 3327218 0.0288896546369529 0.18788802575218308 chr14 107349540 3352248 0.03122740907879065 0.21189210777732903 chr15 102531392 3151752 0.030739385650786835 0.19455516186404345 chr16 90354753 2957023 0.032726811836893625 0.21575485960085997 chr17 81195210 2688541 0.033112064122994445 0.21578910208897628 chr18 78077248 2859444 0.036623268279127874 0.5610553442388877 chr19 59128983 1941882 0.032841457800821636 0.40090245060667046 chr20 63025520 2165605 0.03436076370333795 0.21242349981471878 chr21 48129895 1381298 0.028699376967267435 0.21060781751712096 chr22 51304566 1171619 0.022836544412050967 0.1661849271657259 chrMT 16571 26121 1.5763080079657232 1.641600781352161 chrX 155270560 5889426 0.037930087970314524 0.2445360168509715 chrY 59373566 305294 0.005141917869645896 0.13342658474594923