BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124865.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 = 4,081,964 number of mapped reads = 4,050,296 (99.22%) number of supplementary alignments = 13,723 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,026,124 number of mapped paired reads (second in pair) = 2,024,172 number of mapped paired reads (both in pair) = 4,040,240 number of mapped paired reads (singletons) = 10,056 number of mapped bases = 371,935,936 bp number of sequenced bases = 371,757,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,005 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 56,807.555 std insert size = 2,253,204.2384 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.7059 >>>>>>> ACTG content number of A's = 107,900,286 bp (29.02%) number of C's = 73,249,033 bp (19.7%) number of T's = 110,371,497 bp (29.69%) number of G's = 79,994,507 bp (21.52%) number of N's = 242,104 bp (0.07%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 2,942,564 number of insertions = 50,788 mapped reads with insertion percentage = 1.23% number of deletions = 109,219 mapped reads with deletion percentage = 2.65% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.1201X std coverageData = 1.1183X There is a 8.36% of reference with a coverageData >= 1X There is a 2.45% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 36172965 0.1451268801452655 1.066184734479208 chr2 243199373 32389522 0.1331809436860678 1.3208340139035548 chr3 198022430 28116724 0.1419875718119407 0.5093448244632567 chr4 191154276 16614355 0.08691594740993396 0.7828109341555759 chr5 180915260 16700233 0.09230969792155731 0.38519425049408057 chr6 171115067 21520412 0.12576573400167035 0.6089134811201843 chr7 159138663 16250492 0.10211529802785889 1.6188021285076815 chr8 146364022 25104965 0.17152415366120508 0.6626919630593365 chr9 141213431 20898631 0.14799322452550565 1.5059432448825956 chr10 135534747 22520781 0.1661624159006251 3.191856258174032 chr11 135006516 16275089 0.12055039624902253 0.566068807129324 chr12 133851895 16020571 0.1196887873720428 0.4456227162027976 chr13 115169878 11962143 0.10386520510163257 0.40763738369679126 chr14 107349540 11825284 0.11015682042046943 0.44744021183333876 chr15 102531392 7655240 0.0746624019305229 0.3468213804761982 chr16 90354753 11640169 0.12882741210083326 1.818248488790768 chr17 81195210 8337163 0.10268047831885649 0.5979547222816862 chr18 78077248 10686713 0.1368735870403629 1.3561814488843322 chr19 59128983 4813068 0.08139947206600864 0.6795715677621486 chr20 63025520 11224735 0.1780982528981911 0.5747578976394275 chr21 48129895 4846972 0.10070605805393924 0.49402968822074067 chr22 51304566 4113207 0.08017233787729537 0.36008566614844356 chrMT 16571 51628 3.115563333534488 2.5414206968043316 chrX 155270560 15572627 0.1002934941433843 0.4538792866094337 chrY 59373566 622247 0.010480202587124378 0.6722360589464708