BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525027.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 = 1,443,460 number of mapped reads = 1,329,650 (92.12%) number of supplementary alignments = 5,854 (0.41%) number of secondary alignments = 0 number of mapped bases = 77,754,437 bp number of sequenced bases = 77,729,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,887 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7007 >>>>>>> ACTG content number of A's = 19,962,790 bp (25.68%) number of C's = 14,542,014 bp (18.71%) number of T's = 24,946,443 bp (32.09%) number of G's = 18,277,449 bp (23.51%) number of N's = 915 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 387,094 number of insertions = 5,389 mapped reads with insertion percentage = 0.4% number of deletions = 14,767 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.41% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.237X There is a 2.24% of reference with a coverageData >= 1X There is a 0.2% 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 6292005 0.025243688359757387 0.39512521619291946 chr2 243199373 6658826 0.02738011170777155 0.271408953858475 chr3 198022430 5199889 0.026259090952474425 0.17766124854368162 chr4 191154276 4991302 0.02611138031774921 0.20990100673308826 chr5 180915260 4801642 0.026540834642694043 0.18038198718520887 chr6 171115067 4543691 0.026553424427552017 0.21358465030665894 chr7 159138663 4313210 0.027103470135349823 0.2570974100948138 chr8 146364022 3981626 0.027203584225090508 0.27970698998019833 chr9 141213431 3116816 0.022071668239545855 0.20298694506643988 chr10 135534747 3738825 0.0275857304695452 0.26060046872735615 chr11 135006516 3670835 0.027190057996904386 0.23283136776372293 chr12 133851895 3349206 0.02502173017423474 0.17733789594270405 chr13 115169878 2359927 0.020490835285941693 0.1576454672216393 chr14 107349540 2203556 0.02052692540648055 0.16313563381891233 chr15 102531392 2180747 0.021269066550856933 0.1622965376227254 chr16 90354753 2338571 0.0258821027378604 0.1860792098659691 chr17 81195210 2024591 0.024934857610442784 0.1912457432432918 chr18 78077248 2164894 0.02772759101345375 0.3353557727866576 chr19 59128983 1537415 0.0260010391181597 0.2709527801094139 chr20 63025520 1662940 0.026385184921917344 0.18510473213940343 chr21 48129895 1051029 0.02183734246667274 0.187830301713218 chr22 51304566 887991 0.017308225548579827 0.14377837655713682 chrMT 16571 1977 0.11930480960714501 0.3540445713042616 chrX 155270560 4419065 0.02846041773791503 0.2019420601678471 chrY 59373566 263861 0.00444408206844103 0.14627378291253806