BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234055.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 = 1,069,439 number of mapped reads = 690,289 (64.55%) number of supplementary alignments = 8,179 (0.76%) number of secondary alignments = 0 number of mapped bases = 44,015,607 bp number of sequenced bases = 43,983,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,575 duplication rate = 9.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4326 >>>>>>> ACTG content number of A's = 12,079,444 bp (27.46%) number of C's = 7,602,729 bp (17.29%) number of T's = 14,636,909 bp (33.28%) number of G's = 9,655,693 bp (21.95%) number of N's = 8,612 bp (0.02%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 379,258 number of insertions = 3,783 mapped reads with insertion percentage = 0.54% number of deletions = 18,283 mapped reads with deletion percentage = 2.61% homopolymer indels = 43.07% >>>>>>> Coverage mean coverageData = 0.0142X std coverageData = 0.2357X There is a 0.87% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 4216302 0.016915913722036425 0.35737557030654166 chr2 243199373 4033091 0.016583476142432326 0.24153412956869347 chr3 198022430 3529908 0.017825798824910897 0.20324228538424557 chr4 191154276 1020474 0.005338483770041325 0.1102762709528153 chr5 180915260 2658406 0.01469420545287335 0.18365672586981688 chr6 171115067 2571459 0.015027659720929192 0.19743253251883294 chr7 159138663 2549272 0.016019186990404714 0.21886537712535753 chr8 146364022 2181626 0.014905479981958954 0.5070036160710646 chr9 141213431 2100200 0.01487252299676792 0.19872864886328312 chr10 135534747 1814399 0.01338696563177264 0.19110198000488854 chr11 135006516 2153982 0.01595465214434539 0.21705654951296588 chr12 133851895 905792 0.006767121227532864 0.1225315536410331 chr13 115169878 1471553 0.012777238506756081 0.17650354330566329 chr14 107349540 2697806 0.025131043877784667 0.2474516495656459 chr15 102531392 1081598 0.01054894485388436 0.15388198996824395 chr16 90354753 1082898 0.011984958887552933 0.17102845395949035 chr17 81195210 1233327 0.015189652197463372 0.1869204917419269 chr18 78077248 657801 0.008425002377132965 0.25916348210456414 chr19 59128983 1216891 0.020580279555966658 0.2471767798461357 chr20 63025520 1125405 0.017856338194432986 0.20723150690568767 chr21 48129895 892850 0.018550840387247886 0.21018387790333612 chr22 51304566 397736 0.007752448388316939 0.12498812386019349 chrMT 16571 26102 1.5751614265886187 1.9873269304542165 chrX 155270560 2270662 0.014623905523365151 0.1879566647390083 chrY 59373566 126067 0.002123284964894984 0.06791443778033128