BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818753.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 = 3,041,565 number of mapped reads = 2,969,657 (97.64%) number of supplementary alignments = 25,916 (0.85%) number of secondary alignments = 0 number of mapped bases = 201,733,197 bp number of sequenced bases = 201,647,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,679,951 duplication rate = 47.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.74 >>>>>>> ACTG content number of A's = 58,557,599 bp (29.04%) number of C's = 42,702,866 bp (21.18%) number of T's = 55,309,714 bp (27.43%) number of G's = 45,064,962 bp (22.35%) number of N's = 12,266 bp (0.01%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,023,656 number of insertions = 28,816 mapped reads with insertion percentage = 0.96% number of deletions = 53,243 mapped reads with deletion percentage = 1.77% homopolymer indels = 37.44% >>>>>>> Coverage mean coverageData = 0.0652X std coverageData = 0.7947X There is a 2.32% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% 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 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 16801196 0.06740683707263462 1.1309419082459957 chr2 243199373 17970468 0.07389191747628396 1.3046696068201238 chr3 198022430 12973896 0.06551730528708288 0.5568268480634719 chr4 191154276 13357090 0.06987596761895089 0.6906182385209778 chr5 180915260 12632046 0.06982299890014806 0.5942646733658334 chr6 171115067 11973324 0.06997235374953861 0.64904979703638 chr7 159138663 11193470 0.07033784115680299 0.6720300749984831 chr8 146364022 10199526 0.06968601887696145 0.6593173249757803 chr9 141213431 8717319 0.06173151475938574 0.6439677167147634 chr10 135534747 9759423 0.07200679689910072 0.8151846841759324 chr11 135006516 9452846 0.07001770196040019 0.6552765833497503 chr12 133851895 9186827 0.06863426924213513 0.622219543073278 chr13 115169878 6527726 0.05667910840367479 0.5202024639564443 chr14 107349540 6090397 0.05673426267126995 0.5842156020640579 chr15 102531392 5799385 0.05656204296924009 0.5265889817950807 chr16 90354753 6084580 0.06734100639951945 0.9246127738988681 chr17 81195210 5492573 0.06764651510846514 0.6082783758310409 chr18 78077248 5528953 0.07081388165730432 0.8517634135266693 chr19 59128983 4062242 0.06870136765247595 0.9977560942243446 chr20 63025520 4392362 0.06969180103551705 0.6197339131233113 chr21 48129895 2732553 0.056774547295397174 0.543969670079867 chr22 51304566 2411501 0.047003633165905744 0.5453465463695332 chrMT 16571 163830 9.886548790054915 10.851279262064718 chrX 155270560 6201774 0.03994172494772995 0.49404247340064644 chrY 59373566 2027890 0.0341547617335297 1.4520331007721812