BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234034.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 = 1,873,701 number of mapped reads = 1,468,421 (78.37%) number of supplementary alignments = 13,253 (0.71%) number of secondary alignments = 0 number of mapped bases = 97,239,485 bp number of sequenced bases = 97,186,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,044 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4838 >>>>>>> ACTG content number of A's = 26,832,153 bp (27.61%) number of C's = 18,079,000 bp (18.6%) number of T's = 30,812,127 bp (31.7%) number of G's = 21,436,967 bp (22.06%) number of N's = 25,764 bp (0.03%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 737,720 number of insertions = 7,121 mapped reads with insertion percentage = 0.48% number of deletions = 30,699 mapped reads with deletion percentage = 2.06% homopolymer indels = 45.34% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.2788X There is a 2.55% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 8402947 0.033712842785655485 0.3240315164231692 chr2 243199373 6285825 0.02584638653653108 0.35892634974609083 chr3 198022430 7970342 0.04024969292620033 0.2390539465958373 chr4 191154276 6781489 0.03547652263870885 0.23031031776029418 chr5 180915260 6092634 0.03367672798856216 0.21836183951902105 chr6 171115067 6571159 0.038401989463616316 0.2664380891930691 chr7 159138663 5073193 0.031879072655021615 0.41339650186161164 chr8 146364022 3570270 0.024393084797847384 0.38132236222279814 chr9 141213431 4191918 0.029684980885423002 0.24764192078920177 chr10 135534747 4550701 0.0335758991751392 0.3081015462993382 chr11 135006516 5289644 0.039180657028435574 0.2979209289234847 chr12 133851895 4193267 0.031327662563163564 0.21270724669013705 chr13 115169878 1074016 0.009325493945561009 0.11729259551168308 chr14 107349540 3699351 0.03446079973887173 0.2302446670410115 chr15 102531392 1792357 0.017481055948211453 0.15715246617907172 chr16 90354753 2861595 0.03167066374471745 0.22431693659026994 chr17 81195210 2157855 0.02657613669574843 0.2108902000268921 chr18 78077248 3121922 0.03998504148097023 0.37741018166582757 chr19 59128983 1846821 0.03123376906381089 0.29913292784150347 chr20 63025520 2009862 0.03188965358794342 0.21755057244918638 chr21 48129895 990558 0.020580930002028885 0.1784763666933687 chr22 51304566 1068983 0.02083602071597292 0.17122903987007604 chrMT 16571 33693 2.033250859936033 2.4244114756930073 chrX 155270560 7341865 0.047284333875011464 0.2729794873695493 chrY 59373566 267218 0.004500622381347282 0.09401684412587608