BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714175.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 1,163,788 number of mapped reads = 906,810 (77.92%) number of supplementary alignments = 31,812 (2.73%) number of secondary alignments = 0 number of mapped bases = 118,167,583 bp number of sequenced bases = 116,072,857 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 792,453 duplication rate = 44.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.8199 >>>>>>> ACTG content number of A's = 33,653,610 bp (28.99%) number of C's = 23,437,872 bp (20.19%) number of T's = 32,067,328 bp (27.63%) number of G's = 26,913,066 bp (23.19%) number of N's = 981 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0398 number of mismatches = 4,234,965 number of insertions = 123,189 mapped reads with insertion percentage = 13.19% number of deletions = 353,664 mapped reads with deletion percentage = 37.3% homopolymer indels = 29.75% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 5.7403X There is a 0.08% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7518157 0.030163042201607995 2.661369201368795 chr2 243199373 13304928 0.054707904201710254 10.539724470638383 chr3 198022430 7488096 0.03781438294641672 3.2545972551593785 chr4 191154276 6366414 0.03330510901048324 3.333357372787067 chr5 180915260 6408450 0.03542238504369394 3.0217325162255073 chr6 171115067 5403601 0.03157875629970095 2.4801715853662567 chr7 159138663 5073802 0.0318828995063255 2.7181364983698324 chr8 146364022 5246262 0.03584393164598879 3.1930239994615044 chr9 141213431 4097426 0.02901583773571793 2.746487352288389 chr10 135534747 5529234 0.04079569352057004 3.8123096156188656 chr11 135006516 5075484 0.037594363223179536 3.0868907369401595 chr12 133851895 4643509 0.03469139529178873 3.2459413592262125 chr13 115169878 3833063 0.033281818706103 3.2491808375582987 chr14 107349540 3890617 0.03624251207783471 3.557571835544578 chr15 102531392 3133148 0.03055793878229996 2.657056836649926 chr16 90354753 2821308 0.031224787920121923 2.7131718200726236 chr17 81195210 2448762 0.030158946568399785 2.778973684813102 chr18 78077248 2573276 0.0329580776207686 2.5345209960660706 chr19 59128983 1736209 0.029363079016596648 3.6680824421737617 chr20 63025520 2459039 0.03901656027590094 3.3240640176695404 chr21 48129895 1041890 0.021647460481681917 1.982992344086142 chr22 51304566 944609 0.018411792042057232 1.7540639581613877 chrMT 16571 3555766 214.57763562850764 1697.7178618623425 chrX 155270560 12865801 0.08286053067625955 3.8649249858194907 chrY 59373566 708732 0.011936827240593903 1.479063543759685