BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238246.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 = 1,230,242 number of mapped reads = 582,672 (47.36%) number of supplementary alignments = 5,272 (0.43%) number of secondary alignments = 0 number of mapped bases = 35,569,809 bp number of sequenced bases = 35,554,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,549 duplication rate = 9.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5778 >>>>>>> ACTG content number of A's = 9,894,627 bp (27.83%) number of C's = 7,122,215 bp (20.03%) number of T's = 10,643,158 bp (29.94%) number of G's = 7,886,510 bp (22.18%) number of N's = 7,665 bp (0.02%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 355,717 number of insertions = 2,895 mapped reads with insertion percentage = 0.49% number of deletions = 9,568 mapped reads with deletion percentage = 1.63% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 0.2986X There is a 0.69% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 2643532 0.010605919413135585 0.297023082598822 chr2 243199373 3663261 0.015062789656123003 0.4356788001808042 chr3 198022430 2125326 0.010732753860257144 0.19198301188092856 chr4 191154276 2330408 0.012191241800941978 0.25309712727224054 chr5 180915260 2317763 0.012811318403986485 0.22740980299767155 chr6 171115067 1974789 0.011540707867647914 0.2902889495828306 chr7 159138663 1753639 0.011019565999495672 0.21113800426735102 chr8 146364022 1689120 0.01154054102175465 0.23405115500371654 chr9 141213431 1396603 0.009890015348469226 0.18541737957116874 chr10 135534747 1459943 0.01077172483304226 0.20372515876212452 chr11 135006516 1882313 0.013942386306746853 0.20494607360419234 chr12 133851895 1760373 0.013151647946411217 0.23315686358269996 chr13 115169878 1153456 0.010015257635334129 0.2626150876814549 chr14 107349540 1100719 0.010253597733162154 0.5648518140917747 chr15 102531392 971560 0.009475732076279624 0.7083455961368006 chr16 90354753 1296029 0.014343783331464589 0.21285254989232222 chr17 81195210 910816 0.011217607541134508 0.20643869243561172 chr18 78077248 973186 0.012464399359977441 0.20783672175643036 chr19 59128983 655850 0.011091853211816615 0.191726067536733 chr20 63025520 719033 0.011408600833440169 0.19618186046389263 chr21 48129895 395484 0.008217013562984087 0.1431232059375437 chr22 51304566 379242 0.007391973650064596 0.13653509489357218 chrMT 16571 8709 0.5255566954317784 1.3278575243420725 chrX 155270560 1911027 0.012307722726059596 0.3030570105139314 chrY 59373566 97628 0.0016443007650913202 0.09933504136586878