BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008825.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 = 1,892,292 number of mapped reads = 736,373 (38.91%) number of supplementary alignments = 7,960 (0.42%) number of secondary alignments = 0 number of mapped bases = 48,213,302 bp number of sequenced bases = 48,187,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,550 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3882 >>>>>>> ACTG content number of A's = 13,278,553 bp (27.56%) number of C's = 9,166,087 bp (19.02%) number of T's = 14,967,171 bp (31.06%) number of G's = 10,717,438 bp (22.24%) number of N's = 58,516 bp (0.12%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 438,284 number of insertions = 3,534 mapped reads with insertion percentage = 0.47% number of deletions = 14,322 mapped reads with deletion percentage = 1.92% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 0.2322X There is a 1.26% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.04% 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 4267265 0.017120378608805952 0.41600798367738095 chr2 243199373 4162517 0.017115656790776347 0.22236157390363215 chr3 198022430 5079489 0.025651079021704763 0.20230759607071339 chr4 191154276 1947368 0.010187415321015367 0.12504194645910835 chr5 180915260 2136951 0.011811889168442728 0.12879184518269327 chr6 171115067 1587930 0.009279895849264986 0.12567528818637727 chr7 159138663 2227553 0.013997560102663424 0.20485312372826361 chr8 146364022 5087774 0.03476109723194133 0.3665746667789534 chr9 141213431 1162490 0.008232148966056918 0.1359509349258397 chr10 135534747 2899843 0.021395568768796978 0.41990873282293467 chr11 135006516 1322462 0.009795542016653478 0.13483467805375773 chr12 133851895 1353515 0.010112034648444835 0.1273767091323993 chr13 115169878 2214144 0.019225026877253443 0.16544510899789258 chr14 107349540 2147686 0.020006476040791605 0.17493872725725915 chr15 102531392 1703082 0.01661034700474953 0.1518413760344077 chr16 90354753 1110195 0.012287068063812868 0.16983345362966992 chr17 81195210 1054487 0.01298705921199046 0.1590578515476619 chr18 78077248 1436378 0.018396883045877846 0.27396564410548824 chr19 59128983 783844 0.013256510770699372 0.2674148109786992 chr20 63025520 881789 0.013990983335004615 0.14221071255024367 chr21 48129895 376130 0.007814893425385615 0.14264876220754416 chr22 51304566 492362 0.00959684562968528 0.11412916593807476 chrMT 16571 263774 15.917808219178083 10.36623051340436 chrX 155270560 2349308 0.015130414935065605 0.1582750659912986 chrY 59373566 164966 0.002778441840599569 0.12654332005317737