BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124825.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 28,917,774 number of mapped reads = 28,604,670 (98.92%) number of supplementary alignments = 105,527 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,332,165 number of mapped paired reads (second in pair) = 14,272,505 number of mapped paired reads (both in pair) = 28,475,376 number of mapped paired reads (singletons) = 129,294 number of mapped bases = 2,483,975,005 bp number of sequenced bases = 2,482,689,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,392,733 duplication rate = 11.78% >>>>>>> Insert size mean insert size = 35,714.81 std insert size = 1,764,473.6542 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.7327 >>>>>>> ACTG content number of A's = 698,496,774 bp (28.13%) number of C's = 462,865,500 bp (18.64%) number of T's = 738,021,227 bp (29.73%) number of G's = 583,285,201 bp (23.49%) number of N's = 20,537 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 18,697,778 number of insertions = 314,389 mapped reads with insertion percentage = 1.07% number of deletions = 766,902 mapped reads with deletion percentage = 2.63% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.8024X std coverageData = 7.4844X There is a 30.61% of reference with a coverageData >= 1X There is a 16.65% of reference with a coverageData >= 2X There is a 9.68% of reference with a coverageData >= 3X There is a 6.05% of reference with a coverageData >= 4X There is a 3.94% of reference with a coverageData >= 5X There is a 2.66% of reference with a coverageData >= 6X There is a 1.84% of reference with a coverageData >= 7X There is a 1.31% of reference with a coverageData >= 8X There is a 0.95% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% 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 0.01% 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 232155753 0.9314149431948657 7.5470288866895645 chr2 243199373 188452463 0.7748887699640574 8.567180461643188 chr3 198022430 199460832 1.007263833698031 2.1220694845476684 chr4 191154276 166783169 0.8725055619472515 4.9743010825215865 chr5 180915260 145710584 0.8054079241297832 1.8800078038595607 chr6 171115067 132983017 0.7771555090470204 10.300256251016839 chr7 159138663 123483598 0.7759497011734979 12.036682480532525 chr8 146364022 167235305 1.1425984522343886 3.4634925865167974 chr9 141213431 125186360 0.8865046271696352 10.394036170972148 chr10 135534747 116035778 0.8561330623209117 16.906235286155773 chr11 135006516 104824379 0.776439405339517 6.89297627470705 chr12 133851895 90602496 0.6768861658626499 1.6584454019947226 chr13 115169878 52838833 0.4587903878824982 1.2230290707908038 chr14 107349540 94926655 0.8842763089622927 2.7293435955769056 chr15 102531392 62672905 0.6112557703303199 1.6373880011899913 chr16 90354753 80021384 0.8856355791266454 9.679295034626673 chr17 81195210 77431365 0.9536444945459222 7.576825434659491 chr18 78077248 71585631 0.9168564829539074 10.589332142372529 chr19 59128983 27662310 0.4678299641987754 4.204003215840295 chr20 63025520 65681914 1.0421479108780063 2.5838012240755392 chr21 48129895 31476291 0.6539862802526372 4.148639159233327 chr22 51304566 19041361 0.3711435937300395 1.3632726599650478 chrMT 16571 551979 33.30993905014785 21.0877766328792 chrX 155270560 98611164 0.6350924734218772 3.080362472331133 chrY 59373566 8559479 0.14416312808295867 8.44356922713692