BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549149.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 20,789,852 number of mapped reads = 18,334,195 (88.19%) number of secondary alignments = 0 number of mapped bases = 727,981,706 bp number of sequenced bases = 727,911,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,386,547 duplication rate = 6.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.132 >>>>>>> ACTG content number of A's = 207,549,360 bp (28.51%) number of C's = 155,280,731 bp (21.33%) number of T's = 210,026,320 bp (28.85%) number of G's = 154,911,206 bp (21.28%) number of N's = 143,495 bp (0.02%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 2,205,048 number of insertions = 18,436 mapped reads with insertion percentage = 0.1% number of deletions = 55,977 mapped reads with deletion percentage = 0.31% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.2352X std coverageData = 1.2462X There is a 14.25% of reference with a coverageData >= 1X There is a 5.24% of reference with a coverageData >= 2X There is a 2.09% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 60247950 0.2417163486224574 2.386590993780079 chr2 243199373 61688853 0.2536554771463165 1.226263801415575 chr3 198022430 49362439 0.24927700867017943 0.7501189020252139 chr4 191154276 45469302 0.23786704096538233 0.7447297435404296 chr5 180915260 44925069 0.2483210592627731 0.7686341706193205 chr6 171115067 42182765 0.24651695341357638 0.9153315302309467 chr7 159138663 41143175 0.25853663857914905 1.870843398484064 chr8 146364022 37288802 0.2547675411652735 1.0346712297253085 chr9 141213431 31536404 0.22332439468877432 1.1535866174139584 chr10 135534747 35544255 0.26225197439590897 1.1405337425638236 chr11 135006516 34137287 0.2528565880479428 1.0970024665243001 chr12 133851895 33656384 0.2514449571296693 0.8079284476601766 chr13 115169878 22406205 0.19454917717287154 0.646661317913679 chr14 107349540 22423585 0.20888384803511967 0.8888989151458478 chr15 102531392 22522496 0.21966439312557076 0.6944616949260266 chr16 90354753 22253342 0.2462885599388446 0.8523806569433261 chr17 81195210 21327559 0.2626701624393853 0.8913728463979477 chr18 78077248 19556702 0.25047888470659213 2.3871493099363965 chr19 59128983 16010991 0.2707807607649873 2.0459390178443844 chr20 63025520 16631763 0.26388934196814245 0.8352111062828429 chr21 48129895 9586365 0.19917693566545283 0.7965512573547652 chr22 51304566 9882152 0.1926173978355065 0.7234458000569084 chrMT 16571 123674 7.463279222738519 10.715215817664122 chrX 155270560 23086514 0.14868571350550935 0.7920327244126808 chrY 59373566 4987673 0.08400494253621216 0.5332526086212827