BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716817.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 = 950,141 number of mapped reads = 863,235 (90.85%) number of supplementary alignments = 5,021 (0.53%) number of secondary alignments = 0 number of mapped bases = 50,412,336 bp number of sequenced bases = 50,397,842 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,430 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9978 >>>>>>> ACTG content number of A's = 12,913,870 bp (25.62%) number of C's = 10,175,006 bp (20.19%) number of T's = 15,394,151 bp (30.55%) number of G's = 11,914,401 bp (23.64%) number of N's = 414 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 252,762 number of insertions = 3,119 mapped reads with insertion percentage = 0.36% number of deletions = 9,066 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1728X There is a 1.46% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 4099478 0.01644721278347387 0.2394691864021022 chr2 243199373 4231914 0.01740100703302389 0.2215680526184728 chr3 198022430 3302116 0.016675464491573 0.14066780599545992 chr4 191154276 3157684 0.016519034081141873 0.15836563906677498 chr5 180915260 3007301 0.016622705016702294 0.14060860677474202 chr6 171115067 2865072 0.016743540181648645 0.14991504021195595 chr7 159138663 2798002 0.017582163550035605 0.20721327346366625 chr8 146364022 2548496 0.017412038595113217 0.19223260439315912 chr9 141213431 2076332 0.014703502246893214 0.14706605126368608 chr10 135534747 2496677 0.0184209367358763 0.19251847910517686 chr11 135006516 2289213 0.01695631490853375 0.16495653833150126 chr12 133851895 2266923 0.016936054584808083 0.14315731390664233 chr13 115169878 1525559 0.013246163202499876 0.1251476034468816 chr14 107349540 1513485 0.014098663114904824 0.13237514449042231 chr15 102531392 1463551 0.014274174683983613 0.13132353096855665 chr16 90354753 1512834 0.016743269720409727 0.1469007268024438 chr17 81195210 1437443 0.01770354433469659 0.15141998701732917 chr18 78077248 1346982 0.017251914411737464 0.23715144139440358 chr19 59128983 1082562 0.0183084833371817 0.20021543123541213 chr20 63025520 1104666 0.017527281012516834 0.1472293554638516 chr21 48129895 665290 0.013822801815794528 0.14004001042138492 chr22 51304566 644941 0.012570830440315975 0.12284354097509502 chrMT 16571 3960 0.238971697543902 0.5238609173962492 chrX 155270560 2795061 0.018001229595616838 0.1518530679489607 chrY 59373566 176794 0.0029776550729663097 0.10106790809873388