BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716316.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 = 1,775,047 number of mapped reads = 1,682,279 (94.77%) number of supplementary alignments = 35,101 (1.98%) number of secondary alignments = 0 number of mapped bases = 134,633,088 bp number of sequenced bases = 134,575,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,724 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8739 >>>>>>> ACTG content number of A's = 35,430,870 bp (26.33%) number of C's = 27,949,551 bp (20.77%) number of T's = 39,750,571 bp (29.54%) number of G's = 31,434,468 bp (23.36%) number of N's = 9,553 bp (0.01%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 802,004 number of insertions = 10,522 mapped reads with insertion percentage = 0.62% number of deletions = 29,808 mapped reads with deletion percentage = 1.74% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.3614X There is a 3.75% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 11694090 0.04691699444151034 0.6971442481112071 chr2 243199373 12100950 0.04975732400428516 0.42727163135105733 chr3 198022430 9499754 0.04797312102472432 0.24466151407713185 chr4 191154276 8735100 0.045696597443627154 0.30509743463627 chr5 180915260 8735841 0.04828692173341265 0.24750644066712996 chr6 171115067 6573958 0.03841834687765981 0.2258894996914101 chr7 159138663 6772826 0.04255927423494817 0.3517546659102561 chr8 146364022 7187383 0.049106214094061997 0.41614446309012887 chr9 141213431 5978480 0.04233648285197461 0.3255547838230453 chr10 135534747 4703363 0.03470226716105502 0.395273337785049 chr11 135006516 5560791 0.04118905638598955 0.3401553826835388 chr12 133851895 6485363 0.04845178321905715 0.24765572193646598 chr13 115169878 3831970 0.033272328377390484 0.20342747247104015 chr14 107349540 4391327 0.04090680779815172 0.2365222157330197 chr15 102531392 4026104 0.03926703735769042 0.22270872559282875 chr16 90354753 4142264 0.04584445048507852 0.2566068479689316 chr17 81195210 3897935 0.04800695755328424 0.2785859258102996 chr18 78077248 2790426 0.035739297573603 0.4769215646957335 chr19 59128983 2870360 0.04854404480455887 0.4789596736699689 chr20 63025520 3135567 0.049750751758970015 0.2578884271638535 chr21 48129895 1287921 0.026759273004854884 0.22402301886630988 chr22 51304566 1725295 0.03362848834936056 0.21143018071564323 chrMT 16571 21287 1.2845935670750106 1.4769651313829142 chrX 155270560 8066012 0.05194810915861964 0.28756731398493374 chrY 59373566 418721 0.0070523134824005684 0.22365283539712694