BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975248.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 103,921,590 number of mapped reads = 103,435,119 (99.53%) number of supplementary alignments = 206,516 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 51,709,037 number of mapped paired reads (second in pair) = 51,726,082 number of mapped paired reads (both in pair) = 103,201,312 number of mapped paired reads (singletons) = 233,807 number of mapped bases = 9,494,289,930 bp number of sequenced bases = 9,491,129,602 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,373,087 duplication rate = 47.04% >>>>>>> Insert size mean insert size = 68,274.6168 std insert size = 2,564,656.636 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 55.7935 >>>>>>> ACTG content number of A's = 2,577,222,001 bp (27.15%) number of C's = 2,035,899,354 bp (21.45%) number of T's = 2,640,769,680 bp (27.82%) number of G's = 2,236,943,360 bp (23.57%) number of N's = 295,207 bp (0%) GC percentage = 45.02% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 55,810,114 number of insertions = 1,073,363 mapped reads with insertion percentage = 1.03% number of deletions = 2,103,812 mapped reads with deletion percentage = 2% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 3.0669X std coverageData = 40.1865X There is a 22.62% of reference with a coverageData >= 1X There is a 12.79% of reference with a coverageData >= 2X There is a 7.64% of reference with a coverageData >= 3X There is a 5.46% of reference with a coverageData >= 4X There is a 4.1% of reference with a coverageData >= 5X There is a 3.41% of reference with a coverageData >= 6X There is a 2.93% of reference with a coverageData >= 7X There is a 2.64% of reference with a coverageData >= 8X There is a 2.42% of reference with a coverageData >= 9X There is a 2.27% of reference with a coverageData >= 10X There is a 2.15% of reference with a coverageData >= 11X There is a 2.06% of reference with a coverageData >= 12X There is a 1.98% of reference with a coverageData >= 13X There is a 1.91% of reference with a coverageData >= 14X There is a 1.85% of reference with a coverageData >= 15X There is a 1.8% of reference with a coverageData >= 16X There is a 1.75% of reference with a coverageData >= 17X There is a 1.71% of reference with a coverageData >= 18X There is a 1.67% of reference with a coverageData >= 19X There is a 1.63% of reference with a coverageData >= 20X There is a 1.6% of reference with a coverageData >= 21X There is a 1.57% of reference with a coverageData >= 22X There is a 1.54% of reference with a coverageData >= 23X There is a 1.51% of reference with a coverageData >= 24X There is a 1.48% of reference with a coverageData >= 25X There is a 1.45% of reference with a coverageData >= 26X There is a 1.43% of reference with a coverageData >= 27X There is a 1.4% of reference with a coverageData >= 28X There is a 1.38% of reference with a coverageData >= 29X There is a 1.36% of reference with a coverageData >= 30X There is a 1.33% of reference with a coverageData >= 31X There is a 1.31% of reference with a coverageData >= 32X There is a 1.29% of reference with a coverageData >= 33X There is a 1.27% of reference with a coverageData >= 34X There is a 1.26% of reference with a coverageData >= 35X There is a 1.24% of reference with a coverageData >= 36X There is a 1.22% of reference with a coverageData >= 37X There is a 1.2% of reference with a coverageData >= 38X There is a 1.19% of reference with a coverageData >= 39X There is a 1.17% of reference with a coverageData >= 40X There is a 1.16% of reference with a coverageData >= 41X There is a 1.14% of reference with a coverageData >= 42X There is a 1.13% of reference with a coverageData >= 43X There is a 1.11% of reference with a coverageData >= 44X There is a 1.1% of reference with a coverageData >= 45X There is a 1.08% of reference with a coverageData >= 46X There is a 1.07% of reference with a coverageData >= 47X There is a 1.06% of reference with a coverageData >= 48X There is a 1.04% of reference with a coverageData >= 49X There is a 1.03% of reference with a coverageData >= 50X There is a 1.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1052770216 4.223741597016923 48.068440137453415 chr2 243199373 717440652 2.9500102864163225 34.308530967328785 chr3 198022430 490442820 2.476703371431206 31.189374032005027 chr4 191154276 372256607 1.947414490482023 38.999642297449455 chr5 180915260 456753487 2.524681925670615 31.85062841265512 chr6 171115067 756527744 4.421163824223615 52.427133913421876 chr7 159138663 455356468 2.861381762394221 37.215142265756775 chr8 146364022 334664660 2.286522708428988 29.48472323944651 chr9 141213431 327292976 2.317718461213509 29.39056679051284 chr10 135534747 377723999 2.7869163248594844 34.744417095569645 chr11 135006516 537734269 3.9830245600886403 44.983745206011314 chr12 133851895 611310418 4.567065845425647 51.55779283579776 chr13 115169878 258993729 2.2487974590022577 31.99288132208449 chr14 107349540 310822203 2.895421843447117 37.32037869681223 chr15 102531392 253892950 2.4762460066864205 31.17718163024183 chr16 90354753 322376964 3.5679026647330883 40.19096596750828 chr17 81195210 350579227 4.3177328687246455 43.05384815289922 chr18 78077248 201442669 2.580043151623377 34.000140893791546 chr19 59128983 463093924 7.8319277705148425 99.0593354552932 chr20 63025520 234915309 3.7273045744009727 45.11212528729938 chr21 48129895 82499605 1.7141031577151788 28.756137810595746 chr22 51304566 104237319 2.031735713347619 25.78923915323294 chrMT 16571 232940 14.057087683302154 23.305329258332634 chrX 155270560 408869522 2.6332713812586235 35.55362630823988 chrY 59373566 12059253 0.203108113802698 4.804388173312069