BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080697.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,961,010 number of mapped reads = 1,613,366 (82.27%) number of supplementary alignments = 16,592 (0.85%) number of secondary alignments = 0 number of mapped bases = 109,473,474 bp number of sequenced bases = 109,433,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,938 duplication rate = 5.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2085 >>>>>>> ACTG content number of A's = 31,674,571 bp (28.94%) number of C's = 19,955,829 bp (18.24%) number of T's = 34,775,885 bp (31.78%) number of G's = 23,025,211 bp (21.04%) number of N's = 1,586 bp (0%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 872,415 number of insertions = 8,542 mapped reads with insertion percentage = 0.52% number of deletions = 23,031 mapped reads with deletion percentage = 1.41% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.0354X std coverageData = 0.3107X There is a 2.66% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 8418465 0.033775101406868714 0.4193877351176236 chr2 243199373 9481080 0.038984804455067405 0.32494669580899677 chr3 198022430 7798702 0.03938292242954498 0.25142564601559647 chr4 191154276 7606714 0.03979358536557142 0.25891037668905637 chr5 180915260 7188180 0.039732303399945365 0.2528785444335089 chr6 171115067 6229248 0.03640385448933027 0.2512762964709606 chr7 159138663 5815832 0.03654568846038376 0.33142916281801305 chr8 146364022 5832596 0.039849929786706734 0.649556827105895 chr9 141213431 4423864 0.03132750170201586 0.24814876161315907 chr10 135534747 5241219 0.03867066649705703 0.2842507744381062 chr11 135006516 4878750 0.036137144669372845 0.26673567251746616 chr12 133851895 4659960 0.034814299790077684 0.2375541472936146 chr13 115169878 3701383 0.032138464191131644 0.22958597806828682 chr14 107349540 3378921 0.03147587777274127 0.2302952930295073 chr15 102531392 3003968 0.029298031962737812 0.21668041448596992 chr16 90354753 2856856 0.031618214926668 0.2282303799092531 chr17 81195210 2629967 0.032390666887861984 0.23981009772592068 chr18 78077248 2914523 0.037328710663572566 0.35949162279341984 chr19 59128983 1811563 0.030637479423584878 0.34345737859701664 chr20 63025520 2222246 0.035259463150799863 0.24163684468268187 chr21 48129895 1494661 0.03105473219918722 0.2309962712610585 chr22 51304566 978929 0.019080738349877086 0.16971703709958608 chrMT 16571 185214 11.176995956791986 6.616627091630215 chrX 155270560 6464987 0.041636914299787414 0.2697175477193002 chrY 59373566 255646 0.004305720832061864 0.10813871784906305