BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230405.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,186,540 number of mapped reads = 1,925,947 (88.08%) number of supplementary alignments = 19,626 (0.9%) number of secondary alignments = 0 number of mapped bases = 127,429,657 bp number of sequenced bases = 127,370,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,544 duplication rate = 8.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5689 >>>>>>> ACTG content number of A's = 35,724,269 bp (28.05%) number of C's = 22,990,274 bp (18.05%) number of T's = 41,006,361 bp (32.19%) number of G's = 27,595,212 bp (21.67%) number of N's = 53,919 bp (0.04%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,046,588 number of insertions = 10,302 mapped reads with insertion percentage = 0.53% number of deletions = 36,080 mapped reads with deletion percentage = 1.85% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.3721X There is a 2.36% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 5852689 0.023481141096133917 0.2522776286542557 chr2 243199373 21581635 0.08874050427753365 0.5623828015402104 chr3 198022430 16684368 0.084254940210561 0.4679182497237876 chr4 191154276 18349513 0.09599321230983084 0.5197236655231607 chr5 180915260 2106598 0.011644114487633602 0.1643246798022345 chr6 171115067 5684107 0.03321803918061757 0.39025876503129053 chr7 159138663 1761601 0.011069597838710006 0.1745835069690361 chr8 146364022 1259199 0.008603200313803894 0.5140002009191387 chr9 141213431 2560550 0.01813248202998481 0.280357203026755 chr10 135534747 13627228 0.1005441652538002 0.5810787274582732 chr11 135006516 9525701 0.07055734258041294 0.43368994979310665 chr12 133851895 2946253 0.022011290912242968 0.24593230342303019 chr13 115169878 4683511 0.04066611063007291 0.32809953419951443 chr14 107349540 721840 0.006724202078555716 0.1486691621503375 chr15 102531392 3113823 0.03036945992111372 0.286122848680343 chr16 90354753 533954 0.005909528633208703 0.12255621460319409 chr17 81195210 2313989 0.028499082642929306 0.26157809055360354 chr18 78077248 525129 0.006725762158010487 0.27567803558940635 chr19 59128983 1685618 0.028507474921393456 0.2702807196849517 chr20 63025520 6850167 0.1086887819410296 0.535790805177196 chr21 48129895 1422241 0.029550054077616416 0.29584350098654943 chr22 51304566 1524312 0.02971103975423942 0.2651416194382889 chrMT 16571 1696 0.10234747450365096 0.39185007053329485 chrX 155270560 1917362 0.012348522475864066 0.17122561814643755 chrY 59373566 196573 0.0033107831185346017 0.16820357360379473