BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695923.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 2,293,032 number of mapped reads = 2,284,865 (99.64%) number of supplementary alignments = 38,846 (1.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,144,687 number of mapped paired reads (second in pair) = 1,140,178 number of mapped paired reads (both in pair) = 2,279,378 number of mapped paired reads (singletons) = 5,487 number of mapped bases = 340,900,732 bp number of sequenced bases = 340,814,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,219 duplication rate = 0.24% >>>>>>> Insert size mean insert size = 34,661.8064 std insert size = 1,768,741.8045 median insert size = 294 >>>>>>> Mapping quality mean mapping quality = 55.1851 >>>>>>> ACTG content number of A's = 102,556,392 bp (30.09%) number of C's = 67,786,060 bp (19.89%) number of T's = 102,370,298 bp (30.04%) number of G's = 68,057,159 bp (19.97%) number of N's = 45,007 bp (0.01%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,078,432 number of insertions = 27,269 mapped reads with insertion percentage = 1.17% number of deletions = 35,437 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.1101X std coverageData = 0.3714X There is a 9.46% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 26738513 0.1072756123644723 0.37799727974591246 chr2 243199373 31887997 0.13111874675762425 0.4048728304335696 chr3 198022430 26032148 0.131460602720611 0.3977668562406671 chr4 191154276 25234560 0.13201148584298475 0.3971807149462051 chr5 180915260 22686829 0.1254003061986037 0.38907049950422207 chr6 171115067 22710031 0.1327178921070697 0.4070361619236842 chr7 159138663 18422861 0.11576609136146883 0.3752915814801815 chr8 146364022 20251014 0.13836060066728695 0.4178380691878315 chr9 141213431 13861233 0.09815803568996209 0.35413389820119284 chr10 135534747 15641284 0.11540423652393729 0.3837237766929346 chr11 135006516 15681833 0.11615611945722679 0.3753214464221756 chr12 133851895 16897787 0.12624241890635915 0.39504230179189415 chr13 115169878 11455768 0.09946843913475362 0.34960058660718546 chr14 107349540 11505018 0.10717342617397335 0.36712807107713563 chr15 102531392 9043434 0.08820161146354084 0.32853938042790415 chr16 90354753 8733026 0.09665264648557005 0.35878605271997077 chr17 81195210 6349609 0.07820176830628309 0.31747793283547654 chr18 78077248 9491413 0.12156438966701286 0.38824672849687586 chr19 59128983 2926925 0.04950068226270694 0.2582634580466855 chr20 63025520 6130334 0.09726748783667315 0.34714195538051335 chr21 48129895 4143971 0.086099730739076 0.34666769360711913 chr22 51304566 2349354 0.04579229848664932 0.24167308433252108 chrMT 16571 12796 0.7721923842858005 0.8587431546729598 chrX 155270560 10841003 0.06982008050978884 0.2899092701128826 chrY 59373566 1871991 0.03152903094956432 0.20128929790170424