BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617668.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 10,425,380 number of mapped reads = 10,337,446 (99.16%) number of supplementary alignments = 79,437 (0.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,169,959 number of mapped paired reads (second in pair) = 5,167,487 number of mapped paired reads (both in pair) = 10,309,940 number of mapped paired reads (singletons) = 27,506 number of mapped bases = 1,005,945,919 bp number of sequenced bases = 1,005,602,725 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 423,811 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 141,510.6671 std insert size = 3,521,190.7629 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.3359 >>>>>>> ACTG content number of A's = 291,433,224 bp (28.98%) number of C's = 211,151,351 bp (21%) number of T's = 286,097,998 bp (28.45%) number of G's = 216,852,104 bp (21.56%) number of N's = 68,048 bp (0.01%) GC percentage = 42.56% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 4,450,080 number of insertions = 149,150 mapped reads with insertion percentage = 1.41% number of deletions = 144,385 mapped reads with deletion percentage = 1.36% homopolymer indels = 39.66% >>>>>>> Coverage mean coverageData = 0.325X std coverageData = 3.5297X There is a 22.93% of reference with a coverageData >= 1X There is a 6.32% of reference with a coverageData >= 2X There is a 1.4% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 95251398 0.3821510960247517 8.619017912204741 chr2 243199373 80795279 0.33221828659895436 2.216145999784317 chr3 198022430 56392014 0.2847758912967587 0.8053372397805677 chr4 191154276 62201259 0.3253982087222574 3.1582132416246385 chr5 180915260 61898352 0.34214002732550036 0.6940943988758189 chr6 171115067 74559777 0.4357288829510262 1.3724121181605802 chr7 159138663 57651943 0.3622748985895401 2.682785347932772 chr8 146364022 49174050 0.3359708849760906 3.5406520374749655 chr9 141213431 43482571 0.30792092998576037 3.7359367339932708 chr10 135534747 52352016 0.3862626902605278 6.997750050800652 chr11 135006516 35505773 0.2629930321289085 1.4281897130352403 chr12 133851895 44352866 0.3313577742025991 0.6841833308628847 chr13 115169878 33670249 0.29235291019410475 0.6456876291099788 chr14 107349540 31011115 0.2888798126195976 0.6836381296722192 chr15 102531392 31214083 0.30443440190493076 0.644836269426488 chr16 90354753 32161045 0.3559419281462703 1.9574566299152345 chr17 81195210 25590071 0.31516724939808644 1.0004670572109158 chr18 78077248 26877247 0.34423916939285565 3.448855838922383 chr19 59128983 20830488 0.3522889612358122 4.301463333250478 chr20 63025520 22094856 0.350569991330496 1.0369556892528535 chr21 48129895 16279191 0.3382345006154699 2.2709077890002254 chr22 51304566 13617734 0.2654292797253172 2.3368264113943136 chrMT 16571 1118276 67.4839176875264 24.17999400614397 chrX 155270560 25551222 0.1645593472452215 0.7896240578117957 chrY 59373566 12313044 0.2073825917749323 4.32113545970853