BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238499.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 = 2,880,970 number of mapped reads = 2,510,218 (87.13%) number of supplementary alignments = 18,492 (0.64%) number of secondary alignments = 0 number of mapped bases = 151,839,072 bp number of sequenced bases = 151,766,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 790,438 duplication rate = 20.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0501 >>>>>>> ACTG content number of A's = 37,219,475 bp (24.52%) number of C's = 26,406,647 bp (17.4%) number of T's = 51,484,854 bp (33.92%) number of G's = 36,645,834 bp (24.15%) number of N's = 9,621 bp (0.01%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 892,423 number of insertions = 9,803 mapped reads with insertion percentage = 0.39% number of deletions = 43,783 mapped reads with deletion percentage = 1.73% homopolymer indels = 40.65% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.8497X There is a 2.08% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 14829208 0.05949516972316791 0.6934648539756446 chr2 243199373 18981908 0.07805080977737554 2.1434340524829554 chr3 198022430 5048512 0.025494647247789052 0.35134757359486857 chr4 191154276 9712999 0.05081235535636148 0.46152264079654676 chr5 180915260 5488099 0.030335191182877554 0.3606164970951931 chr6 171115067 15111442 0.08831158041740415 0.91668361161913 chr7 159138663 9613169 0.06040750134993908 0.8894985767453796 chr8 146364022 12652230 0.08644357969337574 0.7310745800629942 chr9 141213431 3493590 0.02473978555198478 0.38569588041609615 chr10 135534747 9742456 0.07188161128894865 0.5943179134215251 chr11 135006516 6276820 0.04649271891439669 0.45949514112805845 chr12 133851895 3859339 0.028832905204666696 0.3616387283775328 chr13 115169878 3386377 0.029403321934577373 0.5798504132741301 chr14 107349540 3758890 0.03501542717369818 0.3956479587777811 chr15 102531392 2592054 0.02528058918774847 0.49895128307116704 chr16 90354753 6493082 0.07186209672887933 0.5912575946065153 chr17 81195210 1851846 0.02280733062947925 0.31073416671555226 chr18 78077248 7112091 0.09109044160982724 1.821194774845772 chr19 59128983 1435257 0.0242733246401346 0.5051765818971612 chr20 63025520 2718523 0.043133686163953903 0.4313047507237048 chr21 48129895 2812750 0.058440808981611116 0.5203002715493705 chr22 51304566 1403375 0.02735380316831839 0.35043588226978173 chrMT 16571 81200 4.900126727415365 4.98970103130756 chrX 155270560 3067701 0.019757132324376238 0.28463179542078765 chrY 59373566 316154 0.005324827550361385 0.3133890508401182