BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068929.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 = 1,555,572 number of mapped reads = 1,053,549 (67.73%) number of supplementary alignments = 6,196 (0.4%) number of secondary alignments = 0 number of mapped bases = 66,811,855 bp number of sequenced bases = 66,780,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,528 duplication rate = 5.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8999 >>>>>>> ACTG content number of A's = 17,644,469 bp (26.42%) number of C's = 11,288,168 bp (16.9%) number of T's = 22,608,483 bp (33.85%) number of G's = 15,089,305 bp (22.6%) number of N's = 150,572 bp (0.23%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 698,527 number of insertions = 5,747 mapped reads with insertion percentage = 0.54% number of deletions = 19,203 mapped reads with deletion percentage = 1.8% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2542X There is a 1.71% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.07% 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 11053988 0.04434888850286957 0.5260820923694284 chr2 243199373 7091558 0.029159441953002074 0.2620032588064478 chr3 198022430 4887716 0.024682638224366806 0.19975811735032933 chr4 191154276 4211497 0.022031926714524554 0.18751204317338105 chr5 180915260 2943479 0.01626993212181217 0.1556885634609714 chr6 171115067 2853422 0.01667545734005995 0.17493967618229703 chr7 159138663 3398873 0.021357933615415634 0.22203367052326045 chr8 146364022 4021015 0.0274727009073309 0.3437710982798991 chr9 141213431 2619164 0.01854755586244484 0.21780540293204437 chr10 135534747 2917090 0.021522820269845637 0.3230043469738337 chr11 135006516 2324494 0.017217643035836876 0.19374804123113182 chr12 133851895 2217816 0.016569178942143478 0.15921693177815605 chr13 115169878 2141075 0.018590581471311447 0.16737847980881201 chr14 107349540 1469853 0.01369221516924991 0.14567393323883823 chr15 102531392 1594208 0.0155484868478134 0.15305124963165143 chr16 90354753 1143753 0.012658470772423007 0.14777591386826902 chr17 81195210 1354435 0.01668121801766385 0.16708222713539497 chr18 78077248 1239362 0.015873535911511635 0.3127002101891677 chr19 59128983 866703 0.01465783708811633 0.2853305276955222 chr20 63025520 1452802 0.023051011717158384 0.19033619167110422 chr21 48129895 1465529 0.030449453504937003 0.22295815553323092 chr22 51304566 557678 0.01086994869033684 0.12432287116380553 chrMT 16571 63524 3.8334439683784924 3.054493793068111 chrX 155270560 2761292 0.017783744709879323 0.17226687044209346 chrY 59373566 161529 0.002720554126730404 0.07520464527075442