BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717075.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 = 463,757 number of mapped reads = 423,693 (91.36%) number of supplementary alignments = 2,602 (0.56%) number of secondary alignments = 0 number of mapped bases = 24,970,049 bp number of sequenced bases = 24,963,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,354 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4345 >>>>>>> ACTG content number of A's = 6,289,287 bp (25.19%) number of C's = 4,658,188 bp (18.66%) number of T's = 7,610,115 bp (30.49%) number of G's = 6,405,284 bp (25.66%) number of N's = 143 bp (0%) GC percentage = 44.32% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 123,201 number of insertions = 1,497 mapped reads with insertion percentage = 0.35% number of deletions = 4,328 mapped reads with deletion percentage = 1.01% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.0081X std coverageData = 0.105X There is a 0.76% of reference with a coverageData >= 1X There is a 0.04% 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 2027204 0.008133195383292546 0.12905279474985534 chr2 243199373 2083279 0.008566136393780916 0.1201247127701629 chr3 198022430 1661554 0.008390736342342633 0.09566426893490196 chr4 191154276 1608110 0.008412628969911193 0.10117053935998647 chr5 180915260 1487568 0.008222457298516443 0.09469916921191272 chr6 171115067 1410227 0.008241395832197523 0.09906668753603036 chr7 159138663 1358591 0.008537152282095018 0.12194542233405525 chr8 146364022 1260502 0.008612102774819894 0.11724127515361084 chr9 141213431 1048652 0.007426007516239726 0.09470793774555235 chr10 135534747 1181237 0.008715381303659349 0.11125526142076227 chr11 135006516 1149488 0.008514314968323455 0.10300224446903901 chr12 133851895 1114927 0.008329557082475373 0.09584952875955041 chr13 115169878 775813 0.006736249212663054 0.08567552301441725 chr14 107349540 753472 0.00701886566071918 0.08824633269725812 chr15 102531392 717470 0.0069975642191612885 0.08817027459227712 chr16 90354753 755665 0.008363312110432088 0.09689296931219324 chr17 81195210 708974 0.008731721982121852 0.10085175003269266 chr18 78077248 659836 0.008451066308074793 0.12724947155461527 chr19 59128983 521568 0.008820851865488706 0.11803222662504498 chr20 63025520 523636 0.00830831701190248 0.09639636989289835 chr21 48129895 342493 0.007116013862070549 0.09246897785297864 chr22 51304566 316851 0.0061758830588295 0.08262623471257102 chrMT 16571 20484 1.236135417295275 1.333997030616515 chrX 155270560 1403416 0.009038519600882486 0.10132731506164122 chrY 59373566 79032 0.0013310974112621095 0.05197761807043291