BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234119.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 = 984,559 number of mapped reads = 703,235 (71.43%) number of supplementary alignments = 2,933 (0.3%) number of secondary alignments = 0 number of mapped bases = 46,560,003 bp number of sequenced bases = 46,535,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,924 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3098 >>>>>>> ACTG content number of A's = 13,382,155 bp (28.76%) number of C's = 7,882,408 bp (16.94%) number of T's = 15,081,993 bp (32.41%) number of G's = 10,182,592 bp (21.88%) number of N's = 6,582 bp (0.01%) GC percentage = 38.82% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 427,002 number of insertions = 3,938 mapped reads with insertion percentage = 0.56% number of deletions = 13,790 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1801X There is a 1.39% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4985922 0.020003649258711377 0.24405133547619431 chr2 243199373 3251980 0.013371662763291745 0.1671100849289524 chr3 198022430 5851051 0.029547415411476367 0.18237927798573494 chr4 191154276 2331297 0.012195892494709351 0.11895372840192878 chr5 180915260 2288568 0.01264994450993244 0.1181635173809121 chr6 171115067 2383512 0.013929293555429576 0.1424576500243932 chr7 159138663 2468887 0.015514061469776203 0.22510751559087017 chr8 146364022 2240848 0.015310101276118253 0.39649797484297583 chr9 141213431 1473361 0.010433575542824959 0.13675416936880597 chr10 135534747 1250514 0.009226519602386537 0.1590782524460664 chr11 135006516 2219328 0.016438673226705593 0.15374350878269907 chr12 133851895 2483751 0.018555964411262164 0.1449569734973283 chr13 115169878 1794785 0.015583805689192447 0.13117441477115344 chr14 107349540 2582321 0.02405525910963382 0.1691407777277161 chr15 102531392 987030 0.009626612696334016 0.10390232425543519 chr16 90354753 652270 0.007218989354107359 0.10662792732147026 chr17 81195210 643948 0.007930861931387333 0.09780874647477687 chr18 78077248 1367953 0.017520507382637256 0.2533426900478344 chr19 59128983 413410 0.00699166430784037 0.1482437092089524 chr20 63025520 478275 0.00758859268436024 0.09492263820678813 chr21 48129895 962465 0.01999723872241982 0.1537454187323537 chr22 51304566 128761 0.0025097376323191195 0.05251334058171938 chrMT 16571 16418 0.9907670025948947 1.2733253318477684 chrX 155270560 3168906 0.02040893006375452 0.15652559635571978 chrY 59373566 134442 0.0022643410031999763 0.059327648414888405