BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716949.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 = 3,921,920 number of mapped reads = 3,215,567 (81.99%) number of supplementary alignments = 16,172 (0.41%) number of secondary alignments = 0 number of mapped bases = 183,918,857 bp number of sequenced bases = 183,871,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 236,447 duplication rate = 5.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3608 >>>>>>> ACTG content number of A's = 47,895,094 bp (26.05%) number of C's = 37,639,886 bp (20.47%) number of T's = 55,911,699 bp (30.41%) number of G's = 42,421,740 bp (23.07%) number of N's = 2,614 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 910,846 number of insertions = 13,679 mapped reads with insertion percentage = 0.42% number of deletions = 30,589 mapped reads with deletion percentage = 0.94% homopolymer indels = 41.02% >>>>>>> Coverage mean coverageData = 0.0594X std coverageData = 0.5458X There is a 4.71% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 18860384 0.07566835309910823 1.106832259267937 chr2 243199373 17325905 0.07124156936046049 0.7522141205810914 chr3 198022430 12291544 0.06207147341844053 0.3112587305737595 chr4 191154276 8436635 0.044135214636788975 0.30196123860332474 chr5 180915260 8037964 0.04442944171763068 0.26736630264998035 chr6 171115067 12499326 0.07304632034536153 0.4007695370887028 chr7 159138663 13520550 0.08496081181730175 0.8648546623438045 chr8 146364022 10640634 0.07269979230278326 0.41849494310127333 chr9 141213431 7623610 0.05398643702665931 0.42283080993785965 chr10 135534747 9941456 0.07334986946188789 0.5232297814169119 chr11 135006516 6043311 0.04476310610074554 0.39260973774404445 chr12 133851895 7401004 0.055292485773174894 0.3021545597963989 chr13 115169878 4052528 0.03518739509301208 0.23176640168126586 chr14 107349540 4027062 0.03751354686755062 0.28830172364259427 chr15 102531392 3873035 0.037774138480437286 0.2592082389126146 chr16 90354753 4003406 0.04430764145855171 0.29877776352275165 chr17 81195210 4137316 0.050955173340890426 0.3038569383339524 chr18 78077248 6284326 0.08048856947416999 0.7413523220167965 chr19 59128983 4806054 0.08128085003592908 0.7353670375980114 chr20 63025520 2798209 0.044398031146748174 0.2686511641327732 chr21 48129895 2321252 0.04822890222386731 0.3119718376049804 chr22 51304566 2356178 0.04592530809051187 0.2658244315017519 chrMT 16571 265650 16.031018043570093 9.396525738550482 chrX 155270560 11895459 0.07661116827298105 0.4270030861115956 chrY 59373566 476059 0.008018029437544648 0.188066113601367