BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004106.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 = 2,382,547 number of mapped reads = 2,181,026 (91.54%) number of supplementary alignments = 17,395 (0.73%) number of secondary alignments = 0 number of mapped bases = 143,025,985 bp number of sequenced bases = 142,962,914 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,414 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0601 >>>>>>> ACTG content number of A's = 38,412,700 bp (26.87%) number of C's = 27,889,966 bp (19.51%) number of T's = 42,773,937 bp (29.92%) number of G's = 33,859,323 bp (23.68%) number of N's = 26,988 bp (0.02%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,158,664 number of insertions = 11,526 mapped reads with insertion percentage = 0.52% number of deletions = 37,680 mapped reads with deletion percentage = 1.71% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.396X There is a 4.04% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 10823844 0.04342554476524253 0.696259333936357 chr2 243199373 12458535 0.05122766085420788 0.555636472423101 chr3 198022430 9542393 0.04818844511705063 0.2459003074777396 chr4 191154276 10241432 0.05357678736938116 0.2738160933878343 chr5 180915260 8336477 0.046079457310566285 0.23953676797739312 chr6 171115067 7602205 0.04442744366865134 0.2642934031187626 chr7 159138663 7358224 0.04623781462836596 0.5176863835958984 chr8 146364022 8623878 0.058920750346693807 0.37819909815014724 chr9 141213431 5714960 0.040470371405394154 0.38566157059807527 chr10 135534747 7122785 0.05255320246401463 0.4070483398037872 chr11 135006516 4897933 0.0362792341074856 0.3067297754657382 chr12 133851895 6133896 0.04582599297529557 0.24090290706746129 chr13 115169878 2965093 0.02574538630665216 0.17688650896989475 chr14 107349540 4093782 0.03813506792856308 0.2545687897160797 chr15 102531392 3663843 0.0357338657803456 0.2165124035130945 chr16 90354753 3828546 0.04237238078665325 0.2760405124788711 chr17 81195210 4267081 0.05255335875108889 0.2715004191685668 chr18 78077248 4657551 0.059653114310586355 0.7117840997335296 chr19 59128983 3269884 0.0553008665817912 0.5515575682169483 chr20 63025520 4240175 0.06727711250934543 0.3017121155523512 chr21 48129895 2180136 0.04529691992887165 0.2595039735622166 chr22 51304566 1548242 0.030177469974114975 0.19153900908635108 chrMT 16571 68487 4.132943093355863 3.279497602354972 chrX 155270560 9010657 0.05803197335026034 0.30914642029181166 chrY 59373566 375946 0.006331875030042831 0.13741944558338373