BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716146.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 = 2,054,626 number of mapped reads = 1,857,659 (90.41%) number of supplementary alignments = 9,576 (0.47%) number of secondary alignments = 0 number of mapped bases = 108,586,019 bp number of sequenced bases = 108,554,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,046 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5529 >>>>>>> ACTG content number of A's = 27,135,976 bp (25%) number of C's = 20,689,569 bp (19.06%) number of T's = 34,276,301 bp (31.58%) number of G's = 26,451,673 bp (24.37%) number of N's = 699 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 539,761 number of insertions = 8,620 mapped reads with insertion percentage = 0.46% number of deletions = 19,959 mapped reads with deletion percentage = 1.07% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.3018X There is a 3.15% of reference with a coverageData >= 1X There is a 0.26% 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 13002259 0.05216540262902695 0.5100531113270312 chr2 243199373 11239557 0.046215402866190775 0.45769604432421457 chr3 198022430 7014577 0.035423143731747965 0.20398365854799366 chr4 191154276 4654732 0.024350655906855048 0.1978124953685035 chr5 180915260 7909066 0.04371696450592393 0.2288234768444169 chr6 171115067 4153934 0.024275676437072603 0.19485124806396392 chr7 159138663 5731414 0.03601522026108765 0.386320088332421 chr8 146364022 4919026 0.03360816362370802 0.27916859988747533 chr9 141213431 2831185 0.020048978202363767 0.22768064821703748 chr10 135534747 4942903 0.03646963682309452 0.2586963279644433 chr11 135006516 5309402 0.03932700552023726 0.3068433619960835 chr12 133851895 4101453 0.03064172531886829 0.1910823591014716 chr13 115169878 3205610 0.027833753544481483 0.18475264601647398 chr14 107349540 2357801 0.02196377366870878 0.16962637725422838 chr15 102531392 4871540 0.047512668120218246 0.2405776254992784 chr16 90354753 3249649 0.03596544611217077 0.22103964388029534 chr17 81195210 4132322 0.05089366724958282 0.27062387328189136 chr18 78077248 3561484 0.04561487618006208 0.5094438506812596 chr19 59128983 1636809 0.027682008330838365 0.35568341178584445 chr20 63025520 2698221 0.042811562681275776 0.2289533873175219 chr21 48129895 1386038 0.02879786045658317 0.19526290095650134 chr22 51304566 1286099 0.025067924753519988 0.17087632153009277 chrMT 16571 32289 1.9485245308068313 1.790550137511023 chrX 155270560 4110450 0.02647282266515945 0.20477576966009325 chrY 59373566 248199 0.004180294644926667 0.11047808664244517