BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714196.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 110,906 number of mapped reads = 18,862 (17.01%) number of supplementary alignments = 681 (0.61%) number of secondary alignments = 0 number of mapped bases = 2,091,710 bp number of sequenced bases = 2,070,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,427 duplication rate = 46.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 30.0056 >>>>>>> ACTG content number of A's = 227,200 bp (10.97%) number of C's = 176,194 bp (8.51%) number of T's = 198,895 bp (9.61%) number of G's = 1,468,368 bp (70.91%) number of N's = 50 bp (0%) GC percentage = 79.42% >>>>>>> Mismatches and indels general error rate = 0.0376 number of mismatches = 62,646 number of insertions = 2,182 mapped reads with insertion percentage = 7.91% number of deletions = 2,881 mapped reads with deletion percentage = 14.88% homopolymer indels = 49.36% >>>>>>> Coverage mean coverageData = 0.0007X std coverageData = 1.5984X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 26129 1.0483023029258571E-4 0.06890955649191702 chr2 243199373 1333827 0.005484500159463816 5.69182059983041 chr3 198022430 16062 8.111202352177983E-5 0.01970412769670912 chr4 191154276 10871 5.687029465142595E-5 0.014482711067546993 chr5 180915260 11324 6.259284042705961E-5 0.019149654680202792 chr6 171115067 19921 1.1641873710630053E-4 0.035251453780115814 chr7 159138663 25009 1.5715225658267595E-4 0.08192500819273404 chr8 146364022 41948 2.866004871060458E-4 0.11883979885956687 chr9 141213431 5778 4.0916787865596154E-5 0.014164672935225147 chr10 135534747 13259 9.78273121356843E-5 0.08596154435283722 chr11 135006516 17225 1.2758643442069121E-4 0.046103587071621266 chr12 133851895 14947 1.116681986459736E-4 0.024893078289128335 chr13 115169878 9628 8.359824779878642E-5 0.019580396870615933 chr14 107349540 14905 1.3884549482000576E-4 0.051707715592288664 chr15 102531392 9237 9.00894820583339E-5 0.023653324404058054 chr16 90354753 8166 9.037709394214159E-5 0.02584083516369204 chr17 81195210 8909 1.0972322135751604E-4 0.035916261796339395 chr18 78077248 3938 5.043722852526769E-5 0.010694455686683549 chr19 59128983 6910 1.1686316336609409E-4 0.02515329078023353 chr20 63025520 17971 2.8513846454579034E-4 0.11514197891719598 chr21 48129895 3970 8.248511657879162E-5 0.021448545595850344 chr22 51304566 1438 2.8028694366111586E-5 0.007672246792800239 chrMT 16571 696 0.042001086234988834 0.3138974451275408 chrX 155270560 466186 0.0030024107596443267 0.38123127372785837 chrY 59373566 3456 5.82077215978572E-5 0.011121513362450408