BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004007.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 = 1,822,322 number of mapped reads = 1,644,648 (90.25%) number of supplementary alignments = 9,655 (0.53%) number of secondary alignments = 0 number of mapped bases = 110,670,352 bp number of sequenced bases = 110,620,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,659 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9838 >>>>>>> ACTG content number of A's = 30,848,566 bp (27.89%) number of C's = 20,272,196 bp (18.33%) number of T's = 35,171,436 bp (31.79%) number of G's = 24,306,671 bp (21.97%) number of N's = 21,831 bp (0.02%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 953,283 number of insertions = 7,813 mapped reads with insertion percentage = 0.47% number of deletions = 28,402 mapped reads with deletion percentage = 1.71% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3309X There is a 3.12% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 7217231 0.028955719231688493 0.613477500990762 chr2 243199373 8377219 0.03444589061502227 0.33671820796292173 chr3 198022430 8075497 0.040780718628692716 0.22310322687573636 chr4 191154276 9776301 0.051143511955756615 0.26516666078575096 chr5 180915260 5878630 0.0324938316425049 0.2008130902918426 chr6 171115067 6718426 0.03926262086552554 0.23733932107202219 chr7 159138663 6595260 0.04144348001717219 0.4759445848302168 chr8 146364022 6523347 0.044569334122288605 0.48789753759872984 chr9 141213431 3394414 0.02403747275285734 0.2535246332795679 chr10 135534747 5767399 0.0425529181826709 0.31229335152149634 chr11 135006516 6265542 0.04640918220569443 0.3133934777170233 chr12 133851895 4734057 0.03536787432109198 0.21340079262544734 chr13 115169878 3693738 0.03207208398709947 0.20320168791523652 chr14 107349540 2530145 0.02356922069717299 0.17985892180724022 chr15 102531392 2638736 0.025735883893978538 0.18051506990671218 chr16 90354753 3447118 0.03815093158408612 0.23265801111098455 chr17 81195210 1493392 0.018392612076500572 0.1656789557212211 chr18 78077248 2801498 0.03588110585045211 0.4750250736093133 chr19 59128983 1811613 0.030638325032581737 0.40190727142488086 chr20 63025520 1630975 0.025878009415868364 0.18907659062566454 chr21 48129895 1703236 0.03538831738569137 0.22193877288898758 chr22 51304566 765426 0.014919256894210937 0.13261138937361383 chrMT 16571 29925 1.805865668939714 1.9002224144802267 chrX 155270560 8518008 0.05485913105485032 0.2827077360879375 chrY 59373566 283219 0.00477011941644199 0.10460115673149745