BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525253.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,106,584 number of mapped reads = 1,010,079 (91.28%) number of supplementary alignments = 4,084 (0.37%) number of secondary alignments = 0 number of mapped bases = 58,420,355 bp number of sequenced bases = 58,400,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,236 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0949 >>>>>>> ACTG content number of A's = 15,058,251 bp (25.78%) number of C's = 10,544,317 bp (18.06%) number of T's = 19,199,820 bp (32.88%) number of G's = 13,597,355 bp (23.28%) number of N's = 1,214 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 293,952 number of insertions = 4,696 mapped reads with insertion percentage = 0.46% number of deletions = 12,229 mapped reads with deletion percentage = 1.2% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.2007X There is a 1.75% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 6299666 0.02527442449180498 0.3349797709089971 chr2 243199373 4935564 0.020294312189694668 0.2564736705411145 chr3 198022430 3462004 0.017482888175849573 0.1404568556696041 chr4 191154276 3386039 0.017713645076922056 0.14575655379858346 chr5 180915260 2597766 0.01435902090293544 0.12669352639461332 chr6 171115067 3848580 0.02249118132887737 0.1741458617932501 chr7 159138663 4292863 0.026975613085300332 0.32359208311420073 chr8 146364022 3404414 0.023259910143764703 0.2080447513163141 chr9 141213431 1932295 0.013683507201237819 0.15140706475150006 chr10 135534747 2995050 0.02209802332091268 0.2098127668945009 chr11 135006516 2840282 0.02103811048645978 0.1781581498897293 chr12 133851895 2595085 0.019387734480710937 0.1480581147767331 chr13 115169878 1281595 0.01112786626378123 0.11196352019252186 chr14 107349540 2704579 0.025194136835611964 0.16871817864656952 chr15 102531392 1267412 0.01236120933577104 0.11940109283808077 chr16 90354753 1480337 0.016383609614869957 0.14526671423607057 chr17 81195210 1010968 0.012451079318595272 0.12106009675655256 chr18 78077248 1308118 0.01675415096597667 0.2583009483364627 chr19 59128983 1001526 0.016937987923790268 0.23406599987340615 chr20 63025520 1218690 0.019336452916215528 0.14813437973854068 chr21 48129895 679646 0.014121077970355016 0.12853815835288668 chr22 51304566 449073 0.008753080573764137 0.09777216158930879 chrMT 16571 83938 5.065355138494961 3.3386186635030084 chrX 155270560 3175575 0.020451880897447657 0.1598835950717203 chrY 59373566 169290 0.0028512688626450363 0.08145697031526411