BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751229.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,858,806 number of mapped reads = 4,475,597 (92.11%) number of supplementary alignments = 174,417 (3.59%) number of secondary alignments = 0 number of mapped bases = 440,131,920 bp number of sequenced bases = 440,004,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,205 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3449 >>>>>>> ACTG content number of A's = 127,851,039 bp (29.06%) number of C's = 92,051,599 bp (20.92%) number of T's = 128,613,982 bp (29.23%) number of G's = 91,485,353 bp (20.79%) number of N's = 2,435 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,532,618 number of insertions = 115,622 mapped reads with insertion percentage = 2.53% number of deletions = 58,047 mapped reads with deletion percentage = 1.27% homopolymer indels = 49.25% >>>>>>> Coverage mean coverageData = 0.1422X std coverageData = 1.1544X There is a 11.15% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 54973559 0.22055535420310948 3.2522157450062443 chr2 243199373 32897872 0.13527120400923073 0.5469842084659696 chr3 198022430 29422364 0.14858096630770565 0.47919884839984694 chr4 191154276 18448319 0.09651010370283321 0.39326807994976615 chr5 180915260 34820817 0.19247031455500216 0.522979338397201 chr6 171115067 25618629 0.14971579913532687 0.8374382684235443 chr7 159138663 23911244 0.15025414659918312 0.6534595518153664 chr8 146364022 21048782 0.14381117512608393 0.5286452977485813 chr9 141213431 19710099 0.1395766596733989 0.6276909769600011 chr10 135534747 22805021 0.1682595902879429 1.4322754471252 chr11 135006516 19685998 0.14581516939523126 0.6464220689179092 chr12 133851895 23404357 0.1748526384329486 0.4937970663897335 chr13 115169878 11806144 0.10251069294351428 0.3729155926946088 chr14 107349540 9702887 0.09038592061037243 0.36939834071171435 chr15 102531392 11350992 0.11070747971509057 0.38914480292207626 chr16 90354753 12514920 0.13850870689669198 0.765004522418032 chr17 81195210 13435525 0.1654718917532204 0.6361973789736114 chr18 78077248 8531468 0.10926957876384168 1.0466024170763562 chr19 59128983 8613577 0.14567436412697982 2.3738582542326383 chr20 63025520 8374076 0.1328680191769937 0.43487402241321194 chr21 48129895 5116594 0.10630802331897878 0.402382903512731 chr22 51304566 5463947 0.10650020896775543 0.3915959471648264 chrMT 16571 476797 28.772976887333293 15.00405418473627 chrX 155270560 17204773 0.11080511978574689 0.4380521332372623 chrY 59373566 793159 0.013358790004292482 0.42267470049752953