BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524878.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 = 3,031,696 number of mapped reads = 2,746,649 (90.6%) number of supplementary alignments = 11,107 (0.37%) number of secondary alignments = 0 number of mapped bases = 157,223,220 bp number of sequenced bases = 157,174,597 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,232 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1221 >>>>>>> ACTG content number of A's = 39,294,868 bp (25%) number of C's = 26,019,949 bp (16.55%) number of T's = 51,339,939 bp (32.66%) number of G's = 40,516,830 bp (25.78%) number of N's = 3,011 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 809,053 number of insertions = 11,449 mapped reads with insertion percentage = 0.42% number of deletions = 30,801 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.4396X There is a 4.28% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 13433222 0.053894437438533005 0.6791101506169833 chr2 243199373 12590929 0.051772045481383706 0.747645528728093 chr3 198022430 9224871 0.046584980297433985 0.2587610336573131 chr4 191154276 9947099 0.05203702061051462 0.33465494218980374 chr5 180915260 9019226 0.04985331806725425 0.25929787372651053 chr6 171115067 8553213 0.04998515414192019 0.3237413564306287 chr7 159138663 9264699 0.0582177757770907 0.5883256734515608 chr8 146364022 8411823 0.057471931182650884 0.5946608910099374 chr9 141213431 5321103 0.03768128118068316 0.3020745750381041 chr10 135534747 7123614 0.05255931897670492 0.45162558424404964 chr11 135006516 5673692 0.04202531972604937 0.33261215385288057 chr12 133851895 7931204 0.059253580235079976 0.2862984582068804 chr13 115169878 4785293 0.04154986601618177 0.2400977898575767 chr14 107349540 4332426 0.04035812356531756 0.2433539040464616 chr15 102531392 5920847 0.057746675281654225 0.2894656174047458 chr16 90354753 5533763 0.06124484674314809 0.31147821111928636 chr17 81195210 6923842 0.08527402047485313 0.36717708621505957 chr18 78077248 2924270 0.03745354856769542 0.49231353696132624 chr19 59128983 3663048 0.0619501268946229 0.5120503909995018 chr20 63025520 3817239 0.060566560974030834 0.30248301318000537 chr21 48129895 2061234 0.042826480298783116 0.3015374388493506 chr22 51304566 1458734 0.028432829935643545 0.19839429200197697 chrMT 16571 46596 2.8119003077665803 2.4461993228037144 chrX 155270560 8715681 0.0561322184965392 0.310151507206501 chrY 59373566 545552 0.009188466126491376 0.31236695564800376