BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716301.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 = 471,191 number of mapped reads = 418,406 (88.8%) number of supplementary alignments = 1,590 (0.34%) number of secondary alignments = 0 number of mapped bases = 24,438,343 bp number of sequenced bases = 24,431,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,597 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5586 >>>>>>> ACTG content number of A's = 5,899,847 bp (24.15%) number of C's = 4,813,394 bp (19.7%) number of T's = 7,578,634 bp (31.02%) number of G's = 6,138,785 bp (25.13%) number of N's = 677 bp (0%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 120,982 number of insertions = 1,384 mapped reads with insertion percentage = 0.33% number of deletions = 4,339 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1054X There is a 0.75% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 1924596 0.007721529407944785 0.15066663318739212 chr2 243199373 2093906 0.008609833052488997 0.12378272623593323 chr3 198022430 1614950 0.00815538926575136 0.09311449302269435 chr4 191154276 1520728 0.00795550082280137 0.09442982713101776 chr5 180915260 1485769 0.008212513416502289 0.09372577461027393 chr6 171115067 1408077 0.008228831187612485 0.09874182233030301 chr7 159138663 1355977 0.008520726355480315 0.11607145396195481 chr8 146364022 1248846 0.008532465717565482 0.10669114962166647 chr9 141213431 1010690 0.007157180395963894 0.0934795729625852 chr10 135534747 1176978 0.00868395762748574 0.10700515961740424 chr11 135006516 1115933 0.008265771409137023 0.10107058885504992 chr12 133851895 1068662 0.007983913862407401 0.09272584338263064 chr13 115169878 763593 0.006630145080122426 0.0839329357930967 chr14 107349540 738826 0.006882432845077864 0.08636640799732301 chr15 102531392 712558 0.006949656940188621 0.0860727860355747 chr16 90354753 725021 0.008024160057191457 0.09431659288082285 chr17 81195210 686676 0.008457099870792871 0.09668454521628629 chr18 78077248 652123 0.008352279527065298 0.13344590568234568 chr19 59128983 518786 0.008773802180903399 0.12428504846082396 chr20 63025520 535091 0.008490068784835096 0.09564402016788283 chr21 48129895 333745 0.0069342557260929 0.08825994621941437 chr22 51304566 295827 0.005766094970962234 0.07844416667337518 chrMT 16571 4519 0.27270532858608415 0.5872228965547636 chrX 155270560 1369003 0.008816887116269819 0.09940048107017771 chrY 59373566 77463 0.0013046715098769712 0.04500591481279577