BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524779.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,503,592 number of mapped reads = 1,363,773 (90.7%) number of supplementary alignments = 4,834 (0.32%) number of secondary alignments = 0 number of mapped bases = 77,182,623 bp number of sequenced bases = 77,158,285 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,882 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2927 >>>>>>> ACTG content number of A's = 18,977,969 bp (24.6%) number of C's = 14,031,270 bp (18.19%) number of T's = 25,290,795 bp (32.78%) number of G's = 18,849,245 bp (24.43%) number of N's = 9,006 bp (0.01%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 393,385 number of insertions = 5,862 mapped reads with insertion percentage = 0.43% number of deletions = 15,033 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2341X There is a 2.23% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6164124 0.02473062644846931 0.29826197443058533 chr2 243199373 6483715 0.026660081068547822 0.4103415191717705 chr3 198022430 5062454 0.025565053413393626 0.17746541874661897 chr4 191154276 4961040 0.025953068400102124 0.20290490317813514 chr5 180915260 4532758 0.025054591856983208 0.17347210577704703 chr6 171115067 4432925 0.025906105626572324 0.19866438973890033 chr7 159138663 4218849 0.02651052183340261 0.2644082237428198 chr8 146364022 3818860 0.0260915213166252 0.2084807410075498 chr9 141213431 3271068 0.023164000597082016 0.19767203120519436 chr10 135534747 3711588 0.02738477093257864 0.2678668781181859 chr11 135006516 3503374 0.02594966601463888 0.20687660435880162 chr12 133851895 3483398 0.02602427107961378 0.1787533782554072 chr13 115169878 2398825 0.020828579847935586 0.15970609560456508 chr14 107349540 2315651 0.02157113109194506 0.16535808480694472 chr15 102531392 2240441 0.02185126873143398 0.16411795979945878 chr16 90354753 2352373 0.02603485618515276 0.19377426372668335 chr17 81195210 2239408 0.0275805432364791 0.18994839993113388 chr18 78077248 2009900 0.025742454447164942 0.29150787566143194 chr19 59128983 1728611 0.029234580273433758 0.2596947537571474 chr20 63025520 1667085 0.026450951931852366 0.18809582035435857 chr21 48129895 1016584 0.021121675000537608 0.1783272105632084 chr22 51304566 966493 0.018838342770505067 0.15337932467383708 chrMT 16571 23396 1.411864099933619 1.3274312217919415 chrX 155270560 4316410 0.027799281460696736 0.19467021401998608 chrY 59373566 263293 0.004434515521604345 0.12427776983043648