BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818977.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 966,172 number of mapped reads = 939,509 (97.24%) number of supplementary alignments = 15,294 (1.58%) number of secondary alignments = 0 number of mapped bases = 86,821,288 bp number of sequenced bases = 86,767,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,455 duplication rate = 28.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7453 >>>>>>> ACTG content number of A's = 25,411,440 bp (29.29%) number of C's = 18,384,817 bp (21.19%) number of T's = 25,134,980 bp (28.97%) number of G's = 17,832,071 bp (20.55%) number of N's = 4,680 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 568,777 number of insertions = 15,019 mapped reads with insertion percentage = 1.56% number of deletions = 28,416 mapped reads with deletion percentage = 2.96% homopolymer indels = 40.2% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.382X There is a 1.68% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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% 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 7873839 0.0315900476733416 0.620491808569704 chr2 243199373 7492818 0.03080936396986517 0.5443043521961792 chr3 198022430 4813884 0.024309791572601144 0.23699446280958858 chr4 191154276 4974303 0.026022452147499958 0.2816064582548682 chr5 180915260 5005850 0.02766958409146912 0.2606694423307257 chr6 171115067 3782200 0.022103255232340236 0.260948942958034 chr7 159138663 4499658 0.028275077314178516 0.46963418572597604 chr8 146364022 8419524 0.057524546571971084 0.3959367404423847 chr9 141213431 3275873 0.02319802710550953 0.340492902173266 chr10 135534747 4899893 0.03615230122501354 0.48329590165534986 chr11 135006516 2761734 0.02045630153140164 0.25356651175163264 chr12 133851895 3323699 0.024831168807882772 0.24274608945951495 chr13 115169878 2140486 0.018585467286854295 0.20651948873746956 chr14 107349540 2244040 0.020904048587446208 0.2328086742207503 chr15 102531392 1837614 0.017922452471921965 0.20412425418018745 chr16 90354753 2777590 0.030740939549688106 0.4605340037012169 chr17 81195210 2521011 0.03104876506877684 0.3048664948345533 chr18 78077248 1955682 0.02504803960303519 0.4001207584169089 chr19 59128983 1682500 0.028454742744349247 0.5686052581314853 chr20 63025520 2725887 0.043250527722738345 0.33870744493350696 chr21 48129895 1246385 0.025896275069787707 0.26434000843804056 chr22 51304566 463306 0.009030502275372528 0.15940199178299821 chrMT 16571 47303 2.8545652042725242 3.1674328011200554 chrX 155270560 5701183 0.03671773322644035 0.33095376167239976 chrY 59373566 355026 0.005979529678240987 0.3673391011051963