BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524808.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 = 1,479,883 number of mapped reads = 1,353,754 (91.48%) number of supplementary alignments = 5,269 (0.36%) number of secondary alignments = 0 number of mapped bases = 77,802,875 bp number of sequenced bases = 77,777,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,195 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5508 >>>>>>> ACTG content number of A's = 18,788,875 bp (24.16%) number of C's = 13,835,135 bp (17.79%) number of T's = 24,493,821 bp (31.49%) number of G's = 20,650,125 bp (26.55%) number of N's = 9,068 bp (0.01%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 397,159 number of insertions = 5,319 mapped reads with insertion percentage = 0.39% number of deletions = 15,634 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.93% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2307X There is a 2.24% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 6173078 0.024766550130280316 0.3143757683356403 chr2 243199373 6472074 0.02661221499119572 0.35083497639476874 chr3 198022430 5088171 0.02569492253983551 0.17879825101495198 chr4 191154276 4978433 0.026044057732718468 0.20330234116874116 chr5 180915260 4625142 0.025565239770265924 0.17565040918937078 chr6 171115067 4328479 0.025295721036651904 0.19344096432187716 chr7 159138663 4236015 0.02661839002631309 0.2750766354649996 chr8 146364022 3901713 0.026657596222656413 0.22082707190180878 chr9 141213431 3387668 0.02398970109295057 0.197959394294588 chr10 135534747 3816473 0.028158631527898895 0.27784295408279397 chr11 135006516 3488563 0.025839960198661818 0.20291259293678882 chr12 133851895 3555396 0.026562164099357726 0.1826456899218052 chr13 115169878 2424740 0.02105359528122449 0.1601212573736544 chr14 107349540 2361591 0.02199907889684483 0.16648787768377138 chr15 102531392 2257178 0.0220145065425426 0.16373952932401784 chr16 90354753 2373205 0.0262654140618369 0.1971989391938785 chr17 81195210 2234180 0.027516155201766212 0.19123958913508388 chr18 78077248 2060024 0.026384434041527693 0.30651492895072746 chr19 59128983 1686954 0.028530069593789564 0.2654849877212376 chr20 63025520 1705648 0.02706281518978344 0.19030226278541593 chr21 48129895 1054270 0.021904681071920062 0.18158712367870283 chr22 51304566 984116 0.01918184046230895 0.15324371318193616 chrMT 16571 20086 1.2121175547643475 1.281340699776244 chrX 155270560 4323115 0.027842464147743138 0.1947911081822468 chrY 59373566 266563 0.004489590535963429 0.1321931382132761