BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124875.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,810,972 number of mapped reads = 3,701,695 (97.13%) number of supplementary alignments = 15,837 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,851,891 number of mapped paired reads (second in pair) = 1,849,804 number of mapped paired reads (both in pair) = 3,688,104 number of mapped paired reads (singletons) = 13,591 number of mapped bases = 331,554,602 bp number of sequenced bases = 331,368,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,135 duplication rate = 4% >>>>>>> Insert size mean insert size = 41,082.005 std insert size = 1,902,686.2212 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.1925 >>>>>>> ACTG content number of A's = 93,897,878 bp (28.34%) number of C's = 63,545,289 bp (19.18%) number of T's = 97,818,075 bp (29.52%) number of G's = 76,102,638 bp (22.97%) number of N's = 4,706 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 2,392,076 number of insertions = 44,641 mapped reads with insertion percentage = 1.17% number of deletions = 111,305 mapped reads with deletion percentage = 2.94% homopolymer indels = 46.89% >>>>>>> Coverage mean coverageData = 0.1071X std coverageData = 0.8174X There is a 7.43% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 27399488 0.10992746132415855 0.8033698968975378 chr2 243199373 28500135 0.11718835722491767 1.1497251720099242 chr3 198022430 20039362 0.10119743505824062 0.4123387024182737 chr4 191154276 17949513 0.09390066168334105 0.8658032561282011 chr5 180915260 18354610 0.1014541835774384 0.4206898554048023 chr6 171115067 17436894 0.10190157012883033 0.5428882706546488 chr7 159138663 15816969 0.09939111402488031 0.8506274645055348 chr8 146364022 15542498 0.10619070033481315 0.49222045513682927 chr9 141213431 13054187 0.09244295608113934 0.955625354516567 chr10 135534747 15585177 0.11499026887916794 1.5350143693315383 chr11 135006516 19658776 0.14561353468302227 0.9709255721828475 chr12 133851895 19915117 0.14878472209900354 0.6606505817763934 chr13 115169878 13535121 0.11752309922564996 0.44565070480301583 chr14 107349540 9522534 0.08870586683464131 0.4166606605089478 chr15 102531392 8825052 0.08607170767758619 0.384211272025278 chr16 90354753 10009144 0.11077606509532487 1.1298826279127487 chr17 81195210 9145642 0.11263770362808348 0.8937422282725196 chr18 78077248 8300843 0.10631577332233841 1.0801233299646003 chr19 59128983 5941879 0.10049012681310619 0.5824180134813574 chr20 63025520 8970299 0.14232804425889703 0.5535957197521866 chr21 48129895 3587423 0.07453627314167213 0.5140426186173225 chr22 51304566 4080537 0.07953555244965915 0.38710299256727404 chrMT 16571 57429 3.465632731880997 2.282902460439701 chrX 155270560 19316271 0.12440395011134113 0.6076075840073891 chrY 59373566 1009702 0.017005918088194332 1.266367582265697