BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354883.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 17,978,854 number of mapped reads = 17,840,502 (99.23%) number of supplementary alignments = 469,809 (2.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,928,445 number of mapped paired reads (second in pair) = 8,912,057 number of mapped paired reads (both in pair) = 17,802,530 number of mapped paired reads (singletons) = 37,972 number of mapped bases = 2,317,354,528 bp number of sequenced bases = 2,315,969,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,262,968 duplication rate = 39.55% >>>>>>> Insert size mean insert size = 237,382.9303 std insert size = 5,570,367.0334 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.9207 >>>>>>> ACTG content number of A's = 662,412,527 bp (28.6%) number of C's = 484,886,243 bp (20.94%) number of T's = 672,742,277 bp (29.05%) number of G's = 495,901,293 bp (21.41%) number of N's = 27,449 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 17,932,164 number of insertions = 468,721 mapped reads with insertion percentage = 2.45% number of deletions = 487,846 mapped reads with deletion percentage = 2.6% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.7486X std coverageData = 20.8002X There is a 29.91% of reference with a coverageData >= 1X There is a 20.22% of reference with a coverageData >= 2X There is a 8.45% of reference with a coverageData >= 3X There is a 5.79% of reference with a coverageData >= 4X There is a 2.41% of reference with a coverageData >= 5X There is a 1.64% of reference with a coverageData >= 6X There is a 0.71% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% 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 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% 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 189579307 0.7605971300669297 20.34566999133759 chr2 243199373 211638824 0.8702276711872937 64.85805875607124 chr3 198022430 151754622 0.7663506704770767 1.8083118017317048 chr4 191154276 157284859 0.8228163255945161 11.296860691211982 chr5 180915260 138272137 0.7642922824752317 1.5218179161159184 chr6 171115067 131576163 0.7689338250967696 3.210862701005013 chr7 159138663 125895646 0.7911065961387397 12.265386036073926 chr8 146364022 113531498 0.7756789984904897 2.9598478932914136 chr9 141213431 99658767 0.705731503683952 10.947235990864597 chr10 135534747 129238614 0.9535459862554655 27.241293410664593 chr11 135006516 104901033 0.7770071853420764 3.693374425440443 chr12 133851895 101847878 0.7608997840486308 1.5768847852769885 chr13 115169878 72053027 0.6256238892603498 1.3339568879050048 chr14 107349540 69876242 0.6509226029287131 3.1364739006210707 chr15 102531392 65556881 0.6393835070531374 1.3424301750280307 chr16 90354753 71755163 0.7941492906300126 5.130590415162824 chr17 81195210 63651409 0.7839305914720831 4.538840846528587 chr18 78077248 63168518 0.8090515434150548 9.417112768823447 chr19 59128983 46064151 0.7790452103666319 10.145004050397398 chr20 63025520 47822198 0.7587751437830264 3.774913193721292 chr21 48129895 32136458 0.6677026409469624 5.913112388308879 chr22 51304566 28277182 0.5511630680201056 2.149938020933896 chrMT 16571 11176170 674.4414941765735 143.26258537893546 chrX 155270560 61828510 0.3981985380873232 1.6882925139419207 chrY 59373566 28809271 0.48522049357789965 13.819280004107625