BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524970.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 = 844,552 number of mapped reads = 780,090 (92.37%) number of supplementary alignments = 2,133 (0.25%) number of secondary alignments = 0 number of mapped bases = 45,955,502 bp number of sequenced bases = 45,940,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,689 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5717 >>>>>>> ACTG content number of A's = 12,005,234 bp (26.13%) number of C's = 8,953,960 bp (19.49%) number of T's = 14,174,434 bp (30.85%) number of G's = 10,806,291 bp (23.52%) number of N's = 549 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 224,229 number of insertions = 2,887 mapped reads with insertion percentage = 0.37% number of deletions = 8,896 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.57% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1644X There is a 1.39% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4876752 0.019565656368013624 0.2918969444196501 chr2 243199373 4081194 0.01678126859315546 0.17808109764057772 chr3 198022430 2521346 0.012732628318923266 0.117801307095518 chr4 191154276 3020544 0.015801603098849853 0.13460638258843635 chr5 180915260 2016142 0.011144123497376618 0.11025731530805612 chr6 171115067 3109580 0.018172450004066563 0.17039960486342837 chr7 159138663 2876033 0.018072496939351566 0.2110117362292 chr8 146364022 3162273 0.02160553499957797 0.17642943453967683 chr9 141213431 1293374 0.009159001313409063 0.1299811404180639 chr10 135534747 2138144 0.0157756150900551 0.15873804873682054 chr11 135006516 1918402 0.014209699330364173 0.146298017468544 chr12 133851895 2505182 0.018716074210230645 0.1439321894519247 chr13 115169878 898245 0.007799304953678947 0.09185799397924438 chr14 107349540 1076243 0.010025594893094092 0.10739855589954977 chr15 102531392 1255484 0.012244874233249462 0.11635825309582185 chr16 90354753 1451368 0.016062995601349273 0.13681343014613595 chr17 81195210 1363716 0.016795522790075918 0.1727992746336842 chr18 78077248 900374 0.011531835753227368 0.19809285462945042 chr19 59128983 1088449 0.018408045340472034 0.19334461240583192 chr20 63025520 1080273 0.017140247315690534 0.13690876161106558 chr21 48129895 664694 0.013810418659753984 0.12535527194939777 chr22 51304566 594436 0.01158641513505835 0.1114028777783151 chrMT 16571 5954 0.35930239575161427 0.657623217694457 chrX 155270560 1938756 0.012486307771415264 0.125751714712607 chrY 59373566 118544 0.0019965787468450187 0.05702952719039841