BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524818.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 = 1,612,118 number of mapped reads = 1,468,132 (91.07%) number of supplementary alignments = 4,759 (0.3%) number of secondary alignments = 0 number of mapped bases = 83,871,034 bp number of sequenced bases = 83,844,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,027 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6183 >>>>>>> ACTG content number of A's = 20,032,892 bp (23.89%) number of C's = 15,584,165 bp (18.59%) number of T's = 27,041,417 bp (32.25%) number of G's = 21,176,352 bp (25.26%) number of N's = 9,999 bp (0.01%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 416,913 number of insertions = 6,515 mapped reads with insertion percentage = 0.44% number of deletions = 16,067 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2343X There is a 2.4% of reference with a coverageData >= 1X There is a 0.23% 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 0.01% 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 6690834 0.026843800722165502 0.26767047843154446 chr2 243199373 7095260 0.02917466403172018 0.37852631324255254 chr3 198022430 5512596 0.027838240344793264 0.18714933624385924 chr4 191154276 5259535 0.02751460814823729 0.2184419670181876 chr5 180915260 4966363 0.02745132168508063 0.1838923554260766 chr6 171115067 4761049 0.02782366908695422 0.20280398814317047 chr7 159138663 4623684 0.029054435376273082 0.2762655726516432 chr8 146364022 4063239 0.027761187103754227 0.20649252908139173 chr9 141213431 3528490 0.02498692918239484 0.20502125212612643 chr10 135534747 4098205 0.03023730143532861 0.29361907951516214 chr11 135006516 3666053 0.02715463748431224 0.21191905885540185 chr12 133851895 3710644 0.027722013199738414 0.18533989802456816 chr13 115169878 2663658 0.023128078680434132 0.168605815155493 chr14 107349540 2580672 0.024039898075017368 0.176645239590094 chr15 102531392 2466947 0.024060406787415896 0.1746074443749739 chr16 90354753 2594510 0.0287147041395819 0.20859351160599493 chr17 81195210 2488242 0.030645182148060213 0.20273116740061015 chr18 78077248 2200318 0.028181295529268655 0.2993584068590563 chr19 59128983 1931890 0.032672471298889075 0.25277278600623027 chr20 63025520 1846960 0.029304954564436755 0.20093408277748304 chr21 48129895 1100227 0.02285953459902624 0.19057023329752654 chr22 51304566 1086427 0.021176029439562944 0.16151925473980067 chrMT 16571 28951 1.7470882867660371 1.6859084197283494 chrX 155270560 4610907 0.029695951376745213 0.20437247344882375 chrY 59373566 295373 0.004974823307732603 0.15188112433757933