BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717072.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 = 837,968 number of mapped reads = 510,210 (60.89%) number of supplementary alignments = 3,001 (0.36%) number of secondary alignments = 0 number of mapped bases = 29,878,077 bp number of sequenced bases = 29,869,861 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,669 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1833 >>>>>>> ACTG content number of A's = 7,957,310 bp (26.64%) number of C's = 5,605,065 bp (18.76%) number of T's = 9,077,173 bp (30.39%) number of G's = 7,230,058 bp (24.21%) number of N's = 255 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 148,444 number of insertions = 2,171 mapped reads with insertion percentage = 0.42% number of deletions = 5,073 mapped reads with deletion percentage = 0.99% homopolymer indels = 40.32% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.1191X There is a 0.89% of reference with a coverageData >= 1X There is a 0.06% 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 2455541 0.009851694612227265 0.14944999579521223 chr2 243199373 2461681 0.010122069681487213 0.13903210320685455 chr3 198022430 1942033 0.009807136494588012 0.10518059570873142 chr4 191154276 1861431 0.009737846513043736 0.11357151873972793 chr5 180915260 1798203 0.009939476636741423 0.10591958388571078 chr6 171115067 1708402 0.009983936715520206 0.10897047559727442 chr7 159138663 1615704 0.010152806172564111 0.13970099054230456 chr8 146364022 1517369 0.010367090076275712 0.1350077430627127 chr9 141213431 1251607 0.00886322916408709 0.10605864034786937 chr10 135534747 1477583 0.010901875959527928 0.13056335000739913 chr11 135006516 1353025 0.010021923682557663 0.11641570385484468 chr12 133851895 1354578 0.010119976261822816 0.10764928846059574 chr13 115169878 901240 0.007825310017259895 0.0939912617693596 chr14 107349540 875470 0.00815532139215501 0.09693073714508949 chr15 102531392 875771 0.008541491370759893 0.09839699361078154 chr16 90354753 928094 0.01027166772289223 0.10952531407284903 chr17 81195210 863477 0.01063458053744796 0.11293477008431446 chr18 78077248 789708 0.01011444460747387 0.15347038874691346 chr19 59128983 640387 0.010830340173447597 0.13146781878997202 chr20 63025520 680398 0.01079559518112663 0.11214400221878072 chr21 48129895 399703 0.008304672179318073 0.10197195669050997 chr22 51304566 379221 0.00739156432977135 0.09168388877086242 chrMT 16571 5135 0.30987870375958 0.5987834212108682 chrX 155270560 1642636 0.010579185133356896 0.11147239537674203 chrY 59373566 99680 0.001678861599790048 0.059874386351861174