BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084343.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,590,479 number of mapped reads = 2,394,898 (92.45%) number of supplementary alignments = 11,095 (0.43%) number of secondary alignments = 0 number of mapped bases = 164,398,841 bp number of sequenced bases = 164,339,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,080 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1967 >>>>>>> ACTG content number of A's = 46,582,562 bp (28.35%) number of C's = 30,418,985 bp (18.51%) number of T's = 52,193,104 bp (31.76%) number of G's = 34,917,360 bp (21.25%) number of N's = 227,276 bp (0.14%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,520,858 number of insertions = 11,234 mapped reads with insertion percentage = 0.47% number of deletions = 34,095 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.92% >>>>>>> Coverage mean coverageData = 0.0531X std coverageData = 0.3517X There is a 4.38% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13430168 0.053882184710785534 0.5415611210527267 chr2 243199373 16341805 0.06719509511235458 0.37642825763819177 chr3 198022430 11469837 0.05792190813939613 0.28424146156166635 chr4 191154276 8277864 0.04330462374799296 0.24963533970902976 chr5 180915260 8456172 0.046741065402664206 0.25183200053992527 chr6 171115067 9177230 0.05363192243030241 0.29619696693959174 chr7 159138663 9650301 0.06064083245439859 0.5256960016841675 chr8 146364022 8408946 0.05745227471270228 0.3975861163328782 chr9 141213431 6218153 0.044033722259747374 0.30286113130759335 chr10 135534747 10659983 0.07865129227710146 0.4518110583885617 chr11 135006516 9515855 0.07048441276715858 0.364801050100774 chr12 133851895 8703405 0.06502265059452464 0.2983278476978504 chr13 115169878 4342496 0.03770513675459481 0.2258697929398596 chr14 107349540 4561146 0.04248873353346461 0.24502422714366054 chr15 102531392 3573441 0.03485216508130505 0.22260527285169054 chr16 90354753 3302306 0.036548226743533904 0.23890071725137457 chr17 81195210 4823435 0.05940541320109893 0.30812352560626277 chr18 78077248 4717167 0.06041666581281144 0.4844900080122386 chr19 59128983 3047489 0.05153968232465625 0.3749399576640837 chr20 63025520 2637833 0.04185341112615969 0.2401648908165549 chr21 48129895 1692928 0.03517414696209082 0.2285599856334106 chr22 51304566 1220609 0.023791430181867242 0.17684954261065974 chrMT 16571 129793 7.832538772554463 5.243943182017323 chrX 155270560 9712881 0.06255455638209845 0.3193839555498026 chrY 59373566 327598 0.005517573258106141 0.1156587979884113