BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,666,182 number of mapped reads = 2,622,536 (98.36%) number of supplementary alignments = 322,186 (12.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,310,961 number of mapped paired reads (second in pair) = 1,311,575 number of mapped paired reads (both in pair) = 2,596,346 number of mapped paired reads (singletons) = 26,190 number of mapped bases = 296,788,242 bp number of sequenced bases = 296,577,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,027,670 duplication rate = 62.94% >>>>>>> Insert size mean insert size = 845,343.1711 std insert size = 8,456,140.3942 median insert size = 145 >>>>>>> Mapping quality mean mapping quality = 52.8876 >>>>>>> ACTG content number of A's = 89,320,683 bp (30.12%) number of C's = 58,371,203 bp (19.68%) number of T's = 88,581,595 bp (29.87%) number of G's = 60,301,183 bp (20.33%) number of N's = 2,418 bp (0%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 2,338,155 number of insertions = 31,417 mapped reads with insertion percentage = 1.16% number of deletions = 91,647 mapped reads with deletion percentage = 3.41% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0959X std coverageData = 1.7656X There is a 2.23% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 1.14% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 23596854 0.0946711944200131 0.9900637162587701 chr2 243199373 27705154 0.11391951244874303 5.3275740743891875 chr3 198022430 20839361 0.10523737639215922 0.9605366055683447 chr4 191154276 20665100 0.1081069198786848 1.0711054595057803 chr5 180915260 17874890 0.0988025554063267 0.9227277437114935 chr6 171115067 17943999 0.10486510226478186 1.0320573108530797 chr7 159138663 16882965 0.1060896496283873 1.0857109765696396 chr8 146364022 15226301 0.10403035385294344 1.187709201771427 chr9 141213431 12779090 0.09049486234776068 0.9894240650688173 chr10 135534747 14219820 0.10491641674735999 1.1833301201869009 chr11 135006516 13861060 0.10266956300094433 0.9680700500262228 chr12 133851895 13590793 0.10153605221651886 0.9491716803052777 chr13 115169878 9842390 0.08545975884423529 0.863884926857942 chr14 107349540 9675402 0.09012988784115888 0.8983789262290796 chr15 102531392 8352337 0.08146126602865199 0.8215838763735311 chr16 90354753 8831883 0.09774674498861172 0.9972919678017232 chr17 81195210 7700426 0.0948384270451422 0.9385386364808556 chr18 78077248 8037408 0.10294174302864773 1.1394248472501458 chr19 59128983 5268862 0.08910794220830756 0.880985060444744 chr20 63025520 6164054 0.09780250920579474 0.9362651519833446 chr21 48129895 4098060 0.08514583295891254 0.9649017882050106 chr22 51304566 3531514 0.06883430219446744 0.8098541475580135 chrMT 16571 443393 26.757166133606905 29.94082890047008 chrX 155270560 7679295 0.049457508235946336 0.642409728065923 chrY 59373566 1977831 0.0333116424234987 0.5788225808615777