BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004031.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 = 1,913,848 number of mapped reads = 1,706,635 (89.17%) number of supplementary alignments = 20,573 (1.07%) number of secondary alignments = 0 number of mapped bases = 114,661,658 bp number of sequenced bases = 114,611,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,740 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5863 >>>>>>> ACTG content number of A's = 33,110,429 bp (28.89%) number of C's = 21,258,330 bp (18.55%) number of T's = 36,344,941 bp (31.71%) number of G's = 23,888,651 bp (20.84%) number of N's = 8,653 bp (0.01%) GC percentage = 39.39% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,061,728 number of insertions = 9,158 mapped reads with insertion percentage = 0.53% number of deletions = 30,765 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.4028X There is a 3.11% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 7626425 0.030597416244752304 0.8142550408941711 chr2 243199373 9353921 0.038461945376808186 0.3748236681505967 chr3 198022430 8982189 0.04535945246202665 0.24412831930586565 chr4 191154276 7923483 0.04145072328907777 0.24363481732559783 chr5 180915260 7439539 0.04112167762962616 0.2367892849302245 chr6 171115067 7457928 0.04358428588874643 0.25644836792617 chr7 159138663 6304636 0.039617248763740086 0.611392151118396 chr8 146364022 7194104 0.049152133848849824 0.5999628311649928 chr9 141213431 4219110 0.029877540472761404 0.32174328532767654 chr10 135534747 6486266 0.047856849579687485 0.3887071076413768 chr11 135006516 3136589 0.023232871219341738 0.23306347971493188 chr12 133851895 6212076 0.04641007137030073 0.2539639605077943 chr13 115169878 3198400 0.02777115036971733 0.19085257432515634 chr14 107349540 2896962 0.026986254435743273 0.2037105850910761 chr15 102531392 4082977 0.03982172601343401 0.22788409068418655 chr16 90354753 3701728 0.04096882429638206 0.26979225843205873 chr17 81195210 2907863 0.03581323331758117 0.23356716042957854 chr18 78077248 3190831 0.04086761613319158 0.6665875264730516 chr19 59128983 2128165 0.0359919094160642 0.55261148049076 chr20 63025520 1933877 0.030684030849725635 0.21251450792243076 chr21 48129895 1397656 0.029039248890943975 0.21120507673747213 chr22 51304566 941411 0.018349458408828564 0.15151376851631507 chrMT 16571 67487 4.072596705087201 3.447030078416468 chrX 155270560 5577003 0.035917967965079796 0.24874241101003255 chrY 59373566 301032 0.005070135083346686 0.11960086496892207