BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173847.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,373,816 number of mapped reads = 10,111,526 (97.47%) number of supplementary alignments = 1,069,947 (10.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,063,451 number of mapped paired reads (second in pair) = 5,048,075 number of mapped paired reads (both in pair) = 9,932,260 number of mapped paired reads (singletons) = 179,266 number of mapped bases = 1,199,973,134 bp number of sequenced bases = 1,199,272,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,038,399 duplication rate = 65.71% >>>>>>> Insert size mean insert size = 984,661.6303 std insert size = 9,093,557.8123 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 52.6293 >>>>>>> ACTG content number of A's = 359,210,176 bp (29.95%) number of C's = 235,963,903 bp (19.68%) number of T's = 358,963,435 bp (29.93%) number of G's = 245,121,122 bp (20.44%) number of N's = 13,579 bp (0%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 12,444,436 number of insertions = 125,469 mapped reads with insertion percentage = 1.2% number of deletions = 289,105 mapped reads with deletion percentage = 2.79% homopolymer indels = 42.72% >>>>>>> Coverage mean coverageData = 0.3876X std coverageData = 5.1731X There is a 7.51% of reference with a coverageData >= 1X There is a 6.06% of reference with a coverageData >= 2X There is a 4.82% of reference with a coverageData >= 3X There is a 4.03% of reference with a coverageData >= 4X There is a 3.15% of reference with a coverageData >= 5X There is a 2.57% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.59% of reference with a coverageData >= 8X There is a 1.19% of reference with a coverageData >= 9X There is a 0.99% of reference with a coverageData >= 10X There is a 0.74% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.48% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 91929723 0.36882444918763113 3.7015952767126574 chr2 243199373 103076859 0.42383686161888257 16.151192392820867 chr3 198022430 106810670 0.5393867250290788 2.229192559256242 chr4 191154276 57917771 0.30298966997735377 2.2410602619466067 chr5 180915260 79152398 0.4375108987489502 1.9467043543145388 chr6 171115067 60594566 0.3541159002672745 2.041188688599223 chr7 159138663 69791503 0.43855780665946653 2.946117594148345 chr8 146364022 66458414 0.454062501780663 2.629709688949085 chr9 141213431 50684963 0.35892452043035483 2.4693939971979137 chr10 135534747 49940763 0.3684720273244764 4.394924843168088 chr11 135006516 44225364 0.32757947771943097 1.769817195955296 chr12 133851895 56134718 0.4193793296688104 1.9049273527871158 chr13 115169878 29258697 0.2540481722139186 1.4775428602262928 chr14 107349540 37739131 0.35155372812962216 1.7497097938844013 chr15 102531392 35617123 0.34737773773714103 1.7308431510792675 chr16 90354753 41679247 0.4612844993334219 2.8175677141083804 chr17 81195210 45981400 0.5663068055369276 2.656645051005343 chr18 78077248 23762015 0.3043398122843674 4.243758810962473 chr19 59128983 19711628 0.3333665995912698 2.72293001574137 chr20 63025520 55708053 0.883896761184993 3.2454256163419988 chr21 48129895 15461522 0.32124570394346386 1.8828827486654736 chr22 51304566 10148626 0.19781136049372292 1.2357378167230593 chrMT 16571 2064997 124.61511073562248 94.92404290737007 chrX 155270560 43974864 0.28321443549891234 1.552417705776162 chrY 59373566 2148119 0.03617972011315608 1.3499152962250254