BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236076.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 = 2,871,584 number of mapped reads = 2,373,258 (82.65%) number of supplementary alignments = 18,930 (0.66%) number of secondary alignments = 0 number of mapped bases = 152,906,267 bp number of sequenced bases = 152,824,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,141 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1851 >>>>>>> ACTG content number of A's = 41,151,521 bp (26.93%) number of C's = 27,196,459 bp (17.8%) number of T's = 49,585,683 bp (32.45%) number of G's = 34,806,965 bp (22.78%) number of N's = 84,166 bp (0.06%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,347,498 number of insertions = 11,578 mapped reads with insertion percentage = 0.48% number of deletions = 46,918 mapped reads with deletion percentage = 1.95% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.4856X There is a 3.54% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 13103589 0.05257194123500298 0.6228880597830039 chr2 243199373 9542140 0.03923587418130391 0.6248721123355943 chr3 198022430 15516515 0.07835736083028574 0.36716340866860203 chr4 191154276 5824379 0.03046951981340977 0.2880995323535076 chr5 180915260 7597831 0.041996628697877667 0.27070466667945225 chr6 171115067 11167615 0.06526377364536812 0.47156172762000736 chr7 159138663 10493474 0.06593918663247787 0.638126497235953 chr8 146364022 10026694 0.0685051822366565 0.8561710983803147 chr9 141213431 6388609 0.04524080290917937 0.4934772978641194 chr10 135534747 2262611 0.016693955240865282 0.41006077541827524 chr11 135006516 9389648 0.06954959122121188 0.5030845630298809 chr12 133851895 5861536 0.04379120669154516 0.2928447517292386 chr13 115169878 3960940 0.03439215243416338 0.2422639495456428 chr14 107349540 6601367 0.06149413402237215 0.3632446369676288 chr15 102531392 3404739 0.03320679582697951 0.24573196566261674 chr16 90354753 6211375 0.06874430833760345 0.38401751641447734 chr17 81195210 5200049 0.06404379026792344 0.3941562760417508 chr18 78077248 5240160 0.06711507044920435 0.9288436549230619 chr19 59128983 2157250 0.03648380016953784 0.5257827995061929 chr20 63025520 3042115 0.0482679873168837 0.2974555701666748 chr21 48129895 2726516 0.05664911589771804 0.3565584751853965 chr22 51304566 1887276 0.03678573170271044 0.24856969807151083 chrMT 16571 173587 10.475348500392252 7.251321957105982 chrX 155270560 4747637 0.030576543293203813 0.2782250172623659 chrY 59373566 378615 0.006376827694668028 0.20162027048564543