BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524711.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 = 3,666,737 number of mapped reads = 3,341,484 (91.13%) number of supplementary alignments = 13,222 (0.36%) number of secondary alignments = 0 number of mapped bases = 193,429,218 bp number of sequenced bases = 193,363,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,712 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0377 >>>>>>> ACTG content number of A's = 49,738,362 bp (25.72%) number of C's = 36,634,884 bp (18.95%) number of T's = 61,969,893 bp (32.05%) number of G's = 45,016,943 bp (23.28%) number of N's = 3,879 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 998,400 number of insertions = 13,043 mapped reads with insertion percentage = 0.39% number of deletions = 40,785 mapped reads with deletion percentage = 1.21% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 0.0625X std coverageData = 0.601X There is a 5.24% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 21225433 0.08515699144436635 1.221920868155015 chr2 243199373 16446662 0.06762625165156162 0.84940812904713 chr3 198022430 14828781 0.07488435022234602 0.32587930839809204 chr4 191154276 10936797 0.057214503535353824 0.3144089429161738 chr5 180915260 8699186 0.04808431306458062 0.2597875739614767 chr6 171115067 10846042 0.0633844943648358 0.3656581028451963 chr7 159138663 14208385 0.08928304870828278 1.0469077843286567 chr8 146364022 11097805 0.07582331264441476 0.5993025015017005 chr9 141213431 6109324 0.0432630519401515 0.3963223511339455 chr10 135534747 10203444 0.07528286454838035 0.5685953544287025 chr11 135006516 8707625 0.06449781283149326 0.4279207976930355 chr12 133851895 8486211 0.06340000640259894 0.3055768088367966 chr13 115169878 5860362 0.05088450297741915 0.27520526767612596 chr14 107349540 7009076 0.06529209161026679 0.30982697696419237 chr15 102531392 5094966 0.04969176659573685 0.2704625378630509 chr16 90354753 4920042 0.05445249792227311 0.32773363476582085 chr17 81195210 3360286 0.04138527383573489 0.25619397985765285 chr18 78077248 2765875 0.03542485257677115 0.8207440075452812 chr19 59128983 3277727 0.05543350880903871 0.7512847071943518 chr20 63025520 4736033 0.07514468742185705 0.3254764078056826 chr21 48129895 2479923 0.05152562664015785 0.3005439438384963 chr22 51304566 2105544 0.04104008988205845 0.2325091813733944 chrMT 16571 135612 8.183694405889808 5.440371964434135 chrX 155270560 9317755 0.060009798380324 0.3356827089994343 chrY 59373566 570322 0.009605655149633425 0.263046785953424