BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777305.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 212,237,082 number of mapped reads = 207,283,362 (97.67%) number of supplementary alignments = 759,098 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 103,976,322 number of mapped paired reads (second in pair) = 103,307,040 number of mapped paired reads (both in pair) = 206,410,686 number of mapped paired reads (singletons) = 872,676 number of mapped bases = 20,022,805,727 bp number of sequenced bases = 20,009,632,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,972,424 duplication rate = 20.73% >>>>>>> Insert size mean insert size = 84,032.3617 std insert size = 2,948,341.9371 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 54.1207 >>>>>>> ACTG content number of A's = 5,557,044,599 bp (27.77%) number of C's = 4,436,758,411 bp (22.17%) number of T's = 5,454,794,327 bp (27.26%) number of G's = 4,559,084,898 bp (22.78%) number of N's = 1,950,207 bp (0.01%) GC percentage = 44.96% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 147,351,989 number of insertions = 3,253,275 mapped reads with insertion percentage = 1.55% number of deletions = 9,485,138 mapped reads with deletion percentage = 4.47% homopolymer indels = 54.19% >>>>>>> Coverage mean coverageData = 6.468X std coverageData = 17.5516X There is a 56.9% of reference with a coverageData >= 1X There is a 47.45% of reference with a coverageData >= 2X There is a 39.67% of reference with a coverageData >= 3X There is a 34.31% of reference with a coverageData >= 4X There is a 30.06% of reference with a coverageData >= 5X There is a 26.68% of reference with a coverageData >= 6X There is a 23.91% of reference with a coverageData >= 7X There is a 21.59% of reference with a coverageData >= 8X There is a 19.61% of reference with a coverageData >= 9X There is a 17.92% of reference with a coverageData >= 10X There is a 16.45% of reference with a coverageData >= 11X There is a 15.16% of reference with a coverageData >= 12X There is a 14.02% of reference with a coverageData >= 13X There is a 13% of reference with a coverageData >= 14X There is a 12.1% of reference with a coverageData >= 15X There is a 11.28% of reference with a coverageData >= 16X There is a 10.55% of reference with a coverageData >= 17X There is a 9.88% of reference with a coverageData >= 18X There is a 9.27% of reference with a coverageData >= 19X There is a 8.72% of reference with a coverageData >= 20X There is a 8.21% of reference with a coverageData >= 21X There is a 7.75% of reference with a coverageData >= 22X There is a 7.32% of reference with a coverageData >= 23X There is a 6.92% of reference with a coverageData >= 24X There is a 6.55% of reference with a coverageData >= 25X There is a 6.21% of reference with a coverageData >= 26X There is a 5.9% of reference with a coverageData >= 27X There is a 5.6% of reference with a coverageData >= 28X There is a 5.33% of reference with a coverageData >= 29X There is a 5.07% of reference with a coverageData >= 30X There is a 4.84% of reference with a coverageData >= 31X There is a 4.61% of reference with a coverageData >= 32X There is a 4.4% of reference with a coverageData >= 33X There is a 4.21% of reference with a coverageData >= 34X There is a 4.02% of reference with a coverageData >= 35X There is a 3.85% of reference with a coverageData >= 36X There is a 3.68% of reference with a coverageData >= 37X There is a 3.53% of reference with a coverageData >= 38X There is a 3.38% of reference with a coverageData >= 39X There is a 3.24% of reference with a coverageData >= 40X There is a 3.11% of reference with a coverageData >= 41X There is a 2.99% of reference with a coverageData >= 42X There is a 2.87% of reference with a coverageData >= 43X There is a 2.76% of reference with a coverageData >= 44X There is a 2.65% of reference with a coverageData >= 45X There is a 2.55% of reference with a coverageData >= 46X There is a 2.46% of reference with a coverageData >= 47X There is a 2.36% of reference with a coverageData >= 48X There is a 2.28% of reference with a coverageData >= 49X There is a 2.2% of reference with a coverageData >= 50X There is a 2.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1869171963 7.499166724242585 21.44208923892752 chr2 243199373 1713199533 7.044424135912554 21.231663615113153 chr3 198022430 1306517180 6.597824195976183 14.962825678024966 chr4 191154276 982805905 5.141427780564009 17.29205440895351 chr5 180915260 1135370473 6.2757031828050325 14.325265109359316 chr6 171115067 1080544790 6.314726160262673 14.556504730062644 chr7 159138663 840310298 5.280365450852129 12.874941660931762 chr8 146364022 1006996010 6.880078835220858 15.882316166854794 chr9 141213431 906599023 6.420062288551009 19.53744186021157 chr10 135534747 1037447641 7.6544772758531066 18.07793920249962 chr11 135006516 1079437187 7.995445101331257 18.565290432433937 chr12 133851895 935593201 6.989764328700763 16.057203603508885 chr13 115169878 520784846 4.5218841509930225 11.927991389799951 chr14 107349540 630078094 5.869406557308024 14.798604201965468 chr15 102531392 663070204 6.466996995417754 15.748775522852423 chr16 90354753 756383106 8.371259738820823 22.596491069655237 chr17 81195210 694619018 8.554926060293457 20.38058251597005 chr18 78077248 518812783 6.644865134078496 19.814780066969774 chr19 59128983 438009878 7.407701871009688 18.68770525116679 chr20 63025520 614787021 9.754572766714181 20.528646635118314 chr21 48129895 259547642 5.392649246377953 29.94823307649365 chr22 51304566 388785129 7.577983000577375 19.258060532895474 chrMT 16571 3915000 236.2561100718122 183.18796685665646 chrX 155270560 540801534 3.482962475307618 8.588589528682952 chrY 59373566 99218268 1.671084873022449 11.340914939297559