BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354876.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 = 173,454,974 number of mapped reads = 172,386,263 (99.38%) number of supplementary alignments = 875,411 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 86,340,276 number of mapped paired reads (second in pair) = 86,045,987 number of mapped paired reads (both in pair) = 171,841,674 number of mapped paired reads (singletons) = 544,589 number of mapped bases = 25,507,622,790 bp number of sequenced bases = 25,497,465,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,903,647 duplication rate = 24.52% >>>>>>> Insert size mean insert size = 35,288.3016 std insert size = 1,870,117.6725 median insert size = 295 >>>>>>> Mapping quality mean mapping quality = 54.502 >>>>>>> ACTG content number of A's = 7,341,178,133 bp (28.79%) number of C's = 5,406,374,608 bp (21.2%) number of T's = 7,284,397,530 bp (28.57%) number of G's = 5,465,040,751 bp (21.43%) number of N's = 474,596 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 217,758,526 number of insertions = 3,561,149 mapped reads with insertion percentage = 1.94% number of deletions = 3,657,264 mapped reads with deletion percentage = 2.03% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 8.2397X std coverageData = 97.1584X There is a 91.53% of reference with a coverageData >= 1X There is a 89.59% of reference with a coverageData >= 2X There is a 86.13% of reference with a coverageData >= 3X There is a 81.03% of reference with a coverageData >= 4X There is a 74.41% of reference with a coverageData >= 5X There is a 66.63% of reference with a coverageData >= 6X There is a 58.17% of reference with a coverageData >= 7X There is a 49.53% of reference with a coverageData >= 8X There is a 41.19% of reference with a coverageData >= 9X There is a 33.5% of reference with a coverageData >= 10X There is a 26.68% of reference with a coverageData >= 11X There is a 20.85% of reference with a coverageData >= 12X There is a 16.02% of reference with a coverageData >= 13X There is a 12.13% of reference with a coverageData >= 14X There is a 9.06% of reference with a coverageData >= 15X There is a 6.7% of reference with a coverageData >= 16X There is a 4.91% of reference with a coverageData >= 17X There is a 3.59% of reference with a coverageData >= 18X There is a 2.61% of reference with a coverageData >= 19X There is a 1.91% of reference with a coverageData >= 20X There is a 1.41% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 0.8% of reference with a coverageData >= 23X There is a 0.62% of reference with a coverageData >= 24X There is a 0.5% of reference with a coverageData >= 25X There is a 0.41% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2151801642 8.633084376548053 229.8067567572445 chr2 243199373 2188575585 8.999100441759774 80.95014350178496 chr3 198022430 1648735048 8.326001493871175 6.490596329609544 chr4 191154276 1604594457 8.39423784064344 69.91845102731257 chr5 180915260 1497002715 8.274607211132992 7.741840723890273 chr6 171115067 1429619967 8.354728733501885 31.28773104163566 chr7 159138663 1409769531 8.85874937255191 115.9892803907827 chr8 146364022 1257975212 8.594839051361953 46.326367370351385 chr9 141213431 1123363036 7.9550721772350395 141.00089829091178 chr10 135534747 1366555662 10.082696077929006 195.87578281287296 chr11 135006516 1196121530 8.859731851757436 44.89444543143699 chr12 133851895 1136249229 8.488854259403649 8.312313123800502 chr13 115169878 771350225 6.697499714291614 5.838659971897381 chr14 107349540 781753599 7.282319039280466 7.667548720252903 chr15 102531392 749508864 7.3100428013305425 6.149917379296845 chr16 90354753 842896088 9.32874099052653 36.139641890021785 chr17 81195210 804088099 9.903146983670588 56.17355999356441 chr18 78077248 697780715 8.937055709238113 106.79329393306058 chr19 59128983 607318809 10.271084977057697 103.04511398522001 chr20 63025520 579290625 9.191366052989329 25.611617670595212 chr21 48129895 360080013 7.481421120906248 35.7821680165207 chr22 51304566 368784836 7.188148438873842 19.975057492163497 chrMT 16571 39179213 2364.3239997586143 255.52655732721342 chrX 155270560 657326046 4.23342355434282 15.911639134440879 chrY 59373566 237902044 4.00686803955821 85.34725360992265