BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716809.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 765,570 number of mapped reads = 643,584 (84.07%) number of supplementary alignments = 3,283 (0.43%) number of secondary alignments = 0 number of mapped bases = 37,480,372 bp number of sequenced bases = 37,469,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,943 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9964 >>>>>>> ACTG content number of A's = 8,988,895 bp (23.99%) number of C's = 6,881,030 bp (18.36%) number of T's = 12,164,260 bp (32.46%) number of G's = 9,434,769 bp (25.18%) number of N's = 530 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 188,154 number of insertions = 2,572 mapped reads with insertion percentage = 0.4% number of deletions = 6,887 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0121X std coverageData = 0.1404X There is a 1.14% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3000209 0.012036916850851096 0.22340346696044563 chr2 243199373 3163120 0.01300628353182473 0.16924061755800812 chr3 198022430 2508887 0.012669711203927757 0.11825842703203693 chr4 191154276 2486128 0.01300587175983445 0.12402013261061312 chr5 180915260 2213509 0.01223505966273934 0.11593406482872433 chr6 171115067 2147953 0.012552681874589104 0.12492512896203137 chr7 159138663 2037238 0.012801653360629278 0.1577994871440864 chr8 146364022 1877956 0.01283072147334131 0.1332514597568273 chr9 141213431 1561292 0.01105625710630882 0.1226914872030396 chr10 135534747 1770128 0.013060326146475192 0.1400641399776655 chr11 135006516 1706346 0.01263898995808469 0.1322915620368467 chr12 133851895 1690272 0.012627927307267485 0.1178303155673525 chr13 115169878 1148178 0.009969429680215516 0.10443217384802636 chr14 107349540 1124873 0.010478601026143196 0.1093230679569661 chr15 102531392 1070661 0.010442275083907961 0.10834406531434178 chr16 90354753 1124219 0.012442278493086024 0.12073769300121281 chr17 81195210 1077626 0.013272039077182015 0.12396272450262227 chr18 78077248 974714 0.01248396972188364 0.18452430637811304 chr19 59128983 831770 0.01406704390636991 0.16052896005052397 chr20 63025520 824555 0.013082875000475998 0.12205104368608422 chr21 48129895 491453 0.010210971787908535 0.11032002222174071 chr22 51304566 446480 0.008702539263269473 0.09748863827400515 chrMT 16571 2803 0.1691509263170599 0.45368897115737 chrX 155270560 2082777 0.013413856432281818 0.1253450406554065 chrY 59373566 117225 0.0019743634734689843 0.0651893274203462