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
A21 F5 I0 R1 24 41.2 1474486 89.7% 1322613 148.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_tpiA 2,795,396 C→A 100% Q382K (CAG→AAG)  gabP → gamma‑aminobutyrate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA2,795,3960CA97.6% 127.9 / ‑4.5 42Q382K (CAG→AAG) gabPgamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (21/20);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAG  >  NC_000913_3_pae_tpiA/2795258‑2795540
                                                                                                                                          |                                                                                                                                                
gTGGCGGTGTTACTCTTTATCGGCGCGGCAGTCTTAACGGTGGTGGTGAAGTATTAAGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGACCTGCTGGTTTATTTAGTCATCGCCGTTCCAAGGTTTCGGAt                                                                                                                                        >  2:174571/1‑149 (MQ=255)
 tGGGGGTGTTACTCTCCACCGGCGCGGCATTGTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGTTCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATg                                                                                                                                       <  2:75721/149‑1 (MQ=255)
 tGGCGGTGTTACTCCCCCCCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTCAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATg                                                                                                                                       <  2:78683/149‑1 (MQ=255)
                  aCCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGc                                                                                                                      >  1:323035/1‑149 (MQ=255)
                   ccGGCGCGGCATTCTTAACGGTGGTAGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTCATCGACAGCTCCGGCGATATCGCCCTGCTGGTTTATTGAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCa                                                                                                                     <  1:663819/149‑1 (MQ=255)
                      gcgcGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAgaa                                                                                                                  >  1:442085/1‑149 (MQ=255)
                          ggCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTCTCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAgaaggaa                                                                                                              <  1:101874/149‑1 (MQ=255)
                            cATTGTTAAGGGTGGTGGTGAACTAGTCGGAGCCGGGGAAGGTATTTAAATTTGTGATTCACAGTTCCGGCGCTATTGTCGTGCTGGGGTTTTTAGTCAGCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGc                                                                                                            <  2:706761/149‑1 (MQ=255)
                            cATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTATAGTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGc                                                                                                            <  1:421684/149‑1 (MQ=255)
                                cTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGAAAAATTCTGCGAGCAGAAGGAAGCGaaa                                                                                                        >  1:634211/1‑149 (MQ=255)
                                 ttAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGTAAGCGAAAt                                                                                                       >  2:453007/1‑149 (MQ=255)
                                       gtggtggtgAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCtt                                                                                                 <  1:76128/149‑1 (MQ=255)
                                             gtgGACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAAt                                                                                           <  2:676712/149‑1 (MQ=255)
                                               gAACTATTACGCGCGTGCGAGGGTATTGAACTTTCTGATCGACAGCTCCGGCGCTATGGCCCTGCTGGTGTATTTCGTCATCTTCGTTTCAAAGTGCCGGATGCTCAAAGTTCTGCGCGCAGATGGATGCGACATTTGCTTGCGACtgt                                                                                         >  2:247332/1‑149 (MQ=255)
                                                aaCTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGATTGCGAAtgtg                                                                                        >  1:498122/1‑149 (MQ=255)
                                                aaCTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCACTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGCAATTCGCTTGCGAAtgtg                                                                                        >  1:272437/1‑149 (MQ=255)
                                                aaCTATTACGCGCCCGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCAGGATTATTTAGTCATCGCCGTTTCAAAGTTGGGGATACGCAAGAGTCGGCGAGCAGGATGAAGCGAGATTGGCTTGCGGAtggg                                                                                        >  2:390013/1‑147 (MQ=255)
                                                  cTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGc                                                                                      >  1:13314/1‑149 (MQ=255)
                                                           gcCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGACGAAGGAAACGAAATTCGCTTGCGAATGTGGCTTTATCCGt                                                                             >  1:316979/1‑149 (MQ=255)
                                                            ccTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTg                                                                            <  2:271065/149‑1 (MQ=255)
                                                              tGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGc                                                                          >  1:458167/1‑149 (MQ=255)
                                                               gCGAAGGGATTTAAATTTGTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCt                                                                         <  2:487660/149‑1 (MQ=255)
                                                                  aatgTATTTAAATGTCTTATCGACAGCTCCGGGGTTATCGTCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                                                                      <  2:698988/146‑1 (MQ=255)
                                                                        tttAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCCCCTGGCt                                                                >  2:238373/1‑149 (MQ=255)
                                                                         ttAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                                               <  1:145531/149‑1 (MQ=255)
                                                                                 cggATCGAGAGCTCCGGCGAGAGCGCGCTGCTGGTTTATGTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGGGCAGAAGGAAGCGACATTCGCTTGTGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCgg                                                       <  2:121472/147‑1 (MQ=255)
                                                                                  tGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                                                      >  1:401822/1‑149 (MQ=255)
                                                                                   gATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGCAAGCGAAATGCGCTTGCGGATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCt                                                     >  1:57603/1‑149 (MQ=255)
                                                                                          cgCTCCGGCCCTAACGACCGGCAGGTGTATTTGGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTAc                                              <  2:216705/148‑1 (MQ=255)
                                                                                          aGCTCCGGCGCTATCGCCCTGCTGGGTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTAc                                              <  1:499967/149‑1 (MQ=255)
                                                                                              ccGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCttt                                          <  1:686013/149‑1 (MQ=255)
                                                                                                    cTAGCGCCCTTGTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGATCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTg                                    <  2:329340/149‑1 (MQ=255)
                                                                                                     tATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATGGGCTTTATTAGCTTTGTGTTgg                                   >  1:275678/1‑149 (MQ=255)
                                                                                                      aTCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGt                                  >  1:375049/1‑149 (MQ=255)
                                                                                                      aTCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGt                                  >  2:145504/1‑149 (MQ=255)
                                                                                                                tgGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGAGGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTa                        >  1:707561/1‑149 (MQ=255)
                                                                                                                  gTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTTTGTTGGTAGTGATGCTAtt                      >  2:288810/1‑149 (MQ=255)
                                                                                                                       tttaGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCCGCAGGAAGTGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATtccgtc                 <  1:167144/149‑1 (MQ=255)
                                                                                                                       tttaGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATtccgtc                 >  1:575542/1‑149 (MQ=255)
                                                                                                                                cGCCGGTTTAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAAc        <  1:518890/149‑1 (MQ=255)
                                                                                                                                     tttCAAAGTTGCCGATGCGCAAAATTCTGCGAGAAGCAGGAACAAAGCTGCCGTTGCTAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTa   <  1:57392/149‑1 (MQ=255)
                                                                                                                                      ttCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACGGTTAg  >  2:659145/1‑149 (MQ=255)
                                                                                                                                          |                                                                                                                                                
GTGGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAG  >  NC_000913_3_pae_tpiA/2795258‑2795540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A