BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716636.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 = 1,234,190 number of mapped reads = 1,128,547 (91.44%) number of supplementary alignments = 3,605 (0.29%) number of secondary alignments = 0 number of mapped bases = 65,154,630 bp number of sequenced bases = 65,133,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,117 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.471 >>>>>>> ACTG content number of A's = 16,389,540 bp (25.16%) number of C's = 12,013,407 bp (18.44%) number of T's = 21,212,745 bp (32.57%) number of G's = 15,516,497 bp (23.82%) number of N's = 1,315 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 333,698 number of insertions = 5,507 mapped reads with insertion percentage = 0.49% number of deletions = 13,036 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.54% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2206X There is a 1.92% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 5465007 0.021925750788801445 0.31761743264866515 chr2 243199373 5143067 0.021147533961775468 0.3463712981348956 chr3 198022430 3705695 0.01871351139363354 0.14773025731803952 chr4 191154276 4016902 0.021013926991620108 0.19015146122842724 chr5 180915260 3660335 0.0202323176054911 0.15313060450893137 chr6 171115067 3457984 0.020208530204999423 0.17422200760695758 chr7 159138663 3684665 0.023153801411540074 0.26128802176525 chr8 146364022 3400654 0.023234220770456827 0.2761012122987059 chr9 141213431 2166042 0.015338781762196543 0.16042655036418363 chr10 135534747 2916293 0.021516939858972104 0.2449631901741521 chr11 135006516 2323257 0.01720848051511825 0.16724953557134017 chr12 133851895 3224729 0.024091769488956433 0.16766959650022945 chr13 115169878 1938723 0.01683359428408876 0.1398660588601758 chr14 107349540 2200408 0.02049760064179129 0.1564580258646966 chr15 102531392 2418197 0.02358494264858903 0.16449906825423283 chr16 90354753 2237449 0.024762936378122796 0.17458947640243289 chr17 81195210 2875663 0.035416658199418416 0.208211432702751 chr18 78077248 1216137 0.015576074095234505 0.23245438384645695 chr19 59128983 1684212 0.028483696396401744 0.2614643792413136 chr20 63025520 2192818 0.034792541180144174 0.2075074649075109 chr21 48129895 846225 0.017582107752364722 0.1791341157128225 chr22 51304566 610559 0.011900675663058918 0.11649674456482233 chrMT 16571 16296 0.9834047432261179 1.1944587205033195 chrX 155270560 3490249 0.022478498177632644 0.17091220769170062 chrY 59373566 263064 0.004430658586348005 0.20663943773519275