BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084362.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,539,362 number of mapped reads = 2,291,361 (90.23%) number of supplementary alignments = 12,771 (0.5%) number of secondary alignments = 0 number of mapped bases = 154,518,993 bp number of sequenced bases = 154,464,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,000 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.182 >>>>>>> ACTG content number of A's = 42,582,045 bp (27.57%) number of C's = 29,992,775 bp (19.42%) number of T's = 47,291,145 bp (30.62%) number of G's = 34,402,054 bp (22.27%) number of N's = 196,567 bp (0.13%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,549,030 number of insertions = 10,754 mapped reads with insertion percentage = 0.46% number of deletions = 30,443 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.3366X There is a 4.18% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 15349108 0.06158102209903822 0.5109150107374979 chr2 243199373 14673152 0.060333839758706945 0.37176995392587936 chr3 198022430 10482871 0.05293779598604057 0.2666555131424054 chr4 191154276 7465694 0.03905585664220245 0.2398005125461473 chr5 180915260 7825003 0.04325231050161275 0.2386077033876894 chr6 171115067 7320664 0.04278211222627169 0.26496983450877537 chr7 159138663 8915252 0.05602191090420308 0.5391937891046531 chr8 146364022 7812252 0.05337549414978498 0.32031143369360443 chr9 141213431 5814907 0.04117814402512464 0.28052188695428515 chr10 135534747 11405512 0.0841519407565648 0.4797455212282932 chr11 135006516 8614516 0.06380814982293151 0.3437844586443639 chr12 133851895 5618314 0.04197410877148956 0.23683589573292552 chr13 115169878 3828738 0.03324426548407041 0.20820504586638433 chr14 107349540 4233945 0.0394407372402341 0.23557696248611762 chr15 102531392 3592488 0.03503793257776116 0.2175114070811538 chr16 90354753 3514731 0.03889923754204718 0.24666248972744123 chr17 81195210 4444500 0.05473845070417331 0.28678129924045975 chr18 78077248 4196883 0.053752957583750906 0.4484208080392711 chr19 59128983 3365366 0.05691567534655551 0.3901470751993992 chr20 63025520 3291842 0.05223030289952388 0.26720069609634906 chr21 48129895 1587835 0.0329906184087873 0.22088860571011 chr22 51304566 1280425 0.024957330308573316 0.18020726855222483 chrMT 16571 10626 0.6412407217428037 0.9166172251204319 chrX 155270560 9537397 0.06142437433084546 0.3114842295843137 chrY 59373566 336972 0.005675454965935514 0.11873516549584787