BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238037.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 = 1,358,933 number of mapped reads = 1,125,589 (82.83%) number of supplementary alignments = 8,551 (0.63%) number of secondary alignments = 0 number of mapped bases = 73,801,396 bp number of sequenced bases = 73,758,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,881 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4888 >>>>>>> ACTG content number of A's = 19,925,770 bp (27.01%) number of C's = 13,149,076 bp (17.83%) number of T's = 23,865,418 bp (32.36%) number of G's = 16,693,063 bp (22.63%) number of N's = 124,874 bp (0.17%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 647,321 number of insertions = 6,296 mapped reads with insertion percentage = 0.55% number of deletions = 25,680 mapped reads with deletion percentage = 2.25% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2643X There is a 2.08% of reference with a coverageData >= 1X There is a 0.22% 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 5773294 0.023162606282934796 0.477493187553538 chr2 243199373 6081649 0.02500684489840358 0.3272615826955367 chr3 198022430 5159837 0.026056831036766894 0.17913207806102882 chr4 191154276 4506937 0.023577484607249906 0.1810691060541681 chr5 180915260 4928737 0.027243345862587823 0.18372309978283866 chr6 171115067 4054402 0.02369400936505492 0.19547234987517817 chr7 159138663 4138678 0.02600674105198433 0.31928375218227023 chr8 146364022 4016942 0.02744487303034075 0.4325718129219597 chr9 141213431 3092191 0.021897286809779447 0.21487609686676676 chr10 135534747 3659589 0.027001112858535087 0.2325160621449875 chr11 135006516 3264967 0.02418377347060789 0.20700985974224043 chr12 133851895 3325817 0.02484699226708744 0.17730232656710734 chr13 115169878 2524537 0.021920115257914922 0.1655650902143783 chr14 107349540 2317922 0.02159228628273582 0.16731507775796128 chr15 102531392 2044604 0.019941248822604497 0.155876445172307 chr16 90354753 1955629 0.021643897360883717 0.1747786054301575 chr17 81195210 1950051 0.024016823159888373 0.18247006079254463 chr18 78077248 1936638 0.02480412731760218 0.3613259225500163 chr19 59128983 1370418 0.023176755805186095 0.3113928839502367 chr20 63025520 1412879 0.02241756989866962 0.17083679831935936 chr21 48129895 953546 0.01981192770106812 0.16543374986455767 chr22 51304566 795962 0.015514447583476294 0.1373739459605671 chrMT 16571 10956 0.6611550298714622 0.8568759089077099 chrX 155270560 4314951 0.027789884959518403 0.19561991529418582 chrY 59373566 210263 0.0035413571083131507 0.09330757950145493