Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A6 F17 I0 R1 19 52.5 1051376 98.5% 1035605 229.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,760,383 A→C 29.8% V289G (GTG→GGG)  selA ← selenocysteine synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,760,3830AC29.8% 33.2 / 2.2 29V289G (GTG→GGG) selAselenocysteine synthase
Reads supporting (aligned to +/- strand):  ref base A (10/9);  new base C (2/7);  total (12/17)
Fisher's exact test for biased strand distribution p-value = 2.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCTGGATTTGAATGACCTCTGCGCTGCGGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTACTTTCATCAACAGTGCGGTATTTTCATTCACCGCCT  >  NC_000913/3760146‑3760611
                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                    
gCCTGGATTTGAATGACCTCTGCGCTGCGGGTAAGCAGGCGCAGGGTCGGTAATTTTTCAATCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGCGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGGTCATCTATTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACCTCTCGCCGGGTAAAATCa                                                                                                                                                                                                                                      >  1:493258/1‑238 (MQ=255)
 ccTGGATTTGAATGACCTCTGCGCTGCGGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCAc                                                                                                                                                                                                                                     <  2:57639/238‑1 (MQ=255)
    ggATTTTAATTACTTCTGGCGTGTGGTTAAGCAGGGGAAGGGTCGGTAATTTTTCACTCAGATCTTCAGGGTGTAAATAAAGAGCCAGCGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCATGCTGCAGCGGGTGGTTTGGCAGGCGGGCGATCATTTCTTTTTTACCAACAATAATTCCTGCCGGCGGCCCGCC‑TAACAGCTTGTCGCCGGAGAAACTCACCAGa                                                                                                                                                                                                                                 <  2:342541/239‑1 (MQ=255)
    ggATTTGAATGACCTCTGCGCTGCGGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTTCCAACAATAATTCCTTCCTGCTGCCCGCC‑TAACCACTTGTCGCCGGAGAAACTCCCCaa                                                                                                                                                                                                                                  >  2:499748/1‑237 (MQ=255)
           aaTGACCTCTGCGCTGCGGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCCGCCGGCCGCC‑CAACAAATTGTGGCCGGAGAAACCCACCAGACTGAcg                                                                                                                                                                                                                           >  2:390356/1‑238 (MQ=255)
                         tgcgGGTAAGCAGGTCAAGGGCCGGTATTTTTTCACTCAGAGCTACAGGGTGTAAATAAAGACGCAACGGGGCTCCCAGCGCCGCGGGGGTC‑ATTTTACCCGCGTGTAATGCACGCTCCAGGGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAAAAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGCCGCCCGCCGCAATCaa                                                                                                                                                                                                             <  2:269345/238‑1 (MQ=255)
                         tgcgGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGGTCATCTCTTTTTTACCAACAATAATTCCTTCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGAATGACGCCCGCCGCAATCaa                                                                                                                                                                                                             >  2:88736/1‑238 (MQ=255)
                           cgGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TACCAACTTGTCCCCGGAGAAACTCACCCGACTGCCCCCCGCCCCAATCAACt                                                                                                                                                                                                           >  2:93892/1‑238 (MQ=255)
                                                 gTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATTTCTTTTTTATCAACAATTAGTCCTCCCTGCGGCCCCCC‑TAACAACTTGTCGCCGGGGAAACTCACCAGACTGACGCCCGCCGGCATCAACTCCTCCCGCAGTGACCCtttacg                                                                                                                                                                                     >  2:152097/1‑235 (MQ=255)
                                                         tccgcaggagCTGCGGGGTAAAAAGAAAGACGCAACGTGGCTTACGGCGCCGGGGGGGTT‑ATTTTATCCGCGTGTAAGCCACGCTTCAGGGGGTGGCTGTGCGGGGGGGCGATCATCTCTTTTTTACAAAAAATAATTCCTGCCTGCGCCCCGCC‑AAACACCTTGTCGCGGGAAAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTa                                                                                                                                                                            <  2:365581/232‑1 (MQ=255)
                                                         tcccgcagtcctgcggggTGTAAAAAGAGACGCAGCGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTCCAGGGGGGGGCTTGGCAGGCGGGCGATCATCTCTTTTTTCCCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTGGTCGCCGGAAAAACTCCCCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTa                                                                                                                                                                            <  2:500506/224‑1 (MQ=255)
                                                                   cTTCGGGGTAAAAAAAAAGCCGCAACGTGGCTCCCAGCGCCGCGAGGGTC‑TTTTTATCCGGGCGAAATGCCCGCTTCGGGGGGTGGCTTGGCGGGGGGGCGATCATCTCTTTTTTACCAACAATAATCCCTGCCGGCGCCCCGCC‑TAACAACTTGTCGCGGGAGAACCCCCCCAGCCTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAg                                                                                                                                                                   <  2:349829/238‑1 (MQ=255)
                                                                                  aacggcGCAGCGTGGCTCCCGGCGCCG‑GGGGGTCTATTTTATCGGCGTTTAGTGCCCGCTTCAGGGGGTGTTTTTGCGGGCGGGCGTTCATCTTTTTTTTCCCAAAAAAAATCCCTCCCTGCGGCCCGCC‑AAACATTTTGTCGCCGGAAAACCCCCCCAGCCTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCa                                                                                                                                                   <  2:304450/234‑1 (MQ=255)
                                                                                        gcacgggggCCTCCAGCGCCGAGAGGTGC‑ATTTGACCCCCGTGTAACGCACGCTCCGGGGGGTGGCTTGGCAGGGGGGCACCCATCTTTTTTTTCCCAACAATAATCCCCCCCGGCGGCCCGCC‑TAAAACCTTGCCCCGGGAAAAACCCCCCAGACGGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCt                                                                                                                                             <  2:493258/232‑1 (MQ=255)
                                                                                            cGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCCACAATAATTCCTTCCTGCGGCCCGCC‑CAACAAATTTTCGCCCGAGAAAATCCCCCGACTGACACCCGCCGCCATCAACTCCCGCTGCATTTGCTCGTTCGGACAAACGCAACGGCCAAAATCGACCAGccggccccccgccaaat                                                                                                                                         >  2:436655/1‑223 (MQ=255)
                                                                                                                                cgcgTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCCACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCCCCGCCTAAAACAATCACTACGGGAACCTCCCGCTCTTTGCCGAg                                                                                                       >  2:381849/1‑238 (MQ=255)
                                                                                                                                                        ggCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTTTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCCCTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCCAGCGCCCACCGTTCCGCCTCATCTAt                                                                               >  2:230588/1‑238 (MQ=255)
                                                                                                                                                                    gggcgATCATCTCTTTTTCACAAAAAATAATCCCGGCCTGCGGCCCGCC‑TAAAAACTTGTCGCCGGAAAACCTCACCAGCCTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGaa                                                                   <  2:449297/238‑1 (MQ=255)
                                                                                                                                                                            atcTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAAt                                                                                                                                         >  1:166308/1‑160 (MQ=255)
                                                                                                                                                                             tttctTTTTTCCCAAAAAAACTCCCTGCCGGCGCCCCGCC‑AAACAACTTGCCGCCGGAGAACCCCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATg                                                         <  2:165259/237‑1 (MQ=255)
                                                                                                                                                                               tctTTTTTACAAACAAAAATCCCGGCCGGCGCCCCGCC‑TAAAAATTTGTCGCGGAAGAAACCCCCCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCt                                                       <  1:285478/239‑1 (MQ=255)
                                                                                                                                                                                ctTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGact                                                          >  1:165259/1‑233 (MQ=255)
                                                                                                                                                                                    tttACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGGCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGt                                                  >  1:456200/1‑239 (MQ=255)
                                                                                                                                                                                      caCCAACAAAAATCCCCGCCTGCGCCCCCCT‑TACCAACTGGCCGCGGGAGAACCTCACCAGACTGCCCCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTa                                                <  1:381849/238‑1 (MQ=255)
                                                                                                                                                                                                acttcccgccgcccgCCCCCC‑CAACACGTTGTCGCCGGAAAACCACACCAGTCGGCCCCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTa                                      <  1:244424/225‑1 (MQ=255)
                                                                                                                                                                                                aatCCCTGCCTG‑GGCCCACCTTAACAATTGGTCGCCGGAGAAACTCCCGACACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTa                                      <  1:34006/239‑1 (MQ=255)
                                                                                                                                                                                                aatCCCTGCCGGCGGCCCGCC‑AAACACCTTGCCGCCGAAAAACCGCCCCAGACTGCCGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTa                                      <  1:502259/239‑1 (MQ=255)
                                                                                                                                                                                                aatACCTGCCGGCGCCCCCCC‑TAACACCTGGCCCCAGGGAAAACGCGCGAGCCTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTa                                      <  2:8078/239‑1 (MQ=255)
                                                                                                                                                                                                       gcctgcGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGccacca                                                                                               >  1:45874/1‑175 (MQ=255)
                                                                                                                                                                                                                                      gaaaaaCTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTACTTTCATCAACAGTGCGGTATTTTCATTCACCGCCt  <  1:499748/235‑1 (MQ=255)
                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                    
GCCTGGATTTGAATGACCTCTGCGCTGCGGGTAAGCAGGCGCAGGGTCGGTAATTTTTCACTCAGAGCTTCAGGGTGTAAATAAAGACGCAACGTGGCTTCCAGCGCCGCGAGGGTC‑ATTTTATCCGCGCGTAATGCACGCTTCAGCGGGTGGCTTTGCAGGCGGGCGATCATCTCTTTTTTACCAACAATAATTCCTGCCTGCGGCCCGCC‑TAACAACTTGTCGCCGGAGAAACTCACCAGACTGACGCCCGCCGCAATCAACTCCTGCGGCATTGGCTCTTTCGGCAAACCGTACTGGCTAAGATCGACCAGCGAGCCACTGCCTAAATCAGTCACTACGGGAACATCCAGCTCTTTGCCGAGCGCCACCAGTTCCGCTTCATCTATCGCTTTGGTGAACCCCTGAATGCTGTAGTTACTGGTATGTACTTTCATCAACAGTGCGGTATTTTCATTCACCGCCT  >  NC_000913/3760146‑3760611

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A