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
A22 F101 I1 R1 19 63.1 2283916 94.2% 2151448 141.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 2,912,587 C→A W355C (TGG→TGT)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA2,912,5870CA97.7% 127.6 / NA 44W355C (TGG→TGT) relA(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (24/19);  minor base G (0/1);  total (24/20)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTCCAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATCGTCAA  >  NC_000913_3_pae_tpiA/2912441‑2912732
                                                                                                                                                  |                                                                                                                                                 
tcgtcAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACa                                                                                                                                                 <  1:384991/149‑1 (MQ=255)
     aaaGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTgcg                                                                                                                                            >  2:111524/1‑149 (MQ=255)
               cTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACAcc                                                                                                                                  <  1:111524/149‑1 (MQ=255)
                     aCTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAAGCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCCCTTTAAATTGATAGAGCGCAGCAAGACCCAGctc                                                                                                                            >  1:145357/1‑149 (MQ=255)
                          gtcgAGCATTTAGCCGGAATCAGACATCTCTACCTGCCACGCAAGCAGTGTACGCAGCAAGGCAATCGGGTCTTCATGTCCCGAACGTGCGCCACCAGCAGCCGCGCCCTCTTTATATTTACAGTACGCAGCAAcaaccaaccttacgt                                                                                                                       >  2:457731/1‑142 (MQ=255)
                               gCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCa                                                                                                                  <  1:242348/149‑1 (MQ=255)
                                cATTTCGCGGGAATCAGCCATCTCTTTCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCAt                                                                                                                 <  2:500781/149‑1 (MQ=255)
                                   ttCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCa                                                                                                              >  2:232462/1‑149 (MQ=255)
                                        cGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGt                                                                                                         <  1:876638/149‑1 (MQ=255)
                                        cGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGt                                                                                                         >  1:844506/1‑149 (MQ=255)
                                          gAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCCTCTGttt                                                                                                       >  1:964173/1‑149 (MQ=255)
                                          gAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGttt                                                                                                       <  1:232462/149‑1 (MQ=255)
                                             tCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCGGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGt                                                                                                    >  1:219869/1‑149 (MQ=255)
                                                 ccATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCAt                                                                                                                 >  2:884864/1‑132 (MQ=255)
                                                 ccATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCAt                                                                                                                 <  1:884864/132‑1 (MQ=255)
                                                 ccATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCgg                                                                                                >  1:795899/1‑149 (MQ=255)
                                                      tctTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTCCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTg                                                                                           >  1:1027438/1‑149 (MQ=255)
                                                              ccACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGCTCTCaa                                                                                   >  1:667558/1‑149 (MQ=255)
                                                                        aGTTTACGCAGCCAGGCCATCCGGTCTTCATGTCCCGAACGTGCGCCGCCACCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCCTCTGTTTGGTGCGGAGTTGGATCTCAACGGTATTTcc                                                                         >  2:556676/1‑149 (MQ=255)
                                                                          tttACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGCTTTGGATCTCAACGGTTTTTCCAc                                                                       >  1:247393/1‑149 (MQ=255)
                                                                          tttACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATACATCTGTTTGGTGCGGATTTGGAGCTCAACGGTTTTTCTAc                                                                       >  1:477593/1‑149 (MQ=255)
                                                                           ttACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCAcc                                                                      <  2:795899/149‑1 (MQ=255)
                                                                            ttcGCACCCAGGCATGTCGGTTCTTATGCTCCGACCGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTTGTGCGGATTTGGATCTCAACGGTTTTTCCAccc                                                                     <  2:1061341/147‑1 (MQ=255)
                                                                                   ccAGGCAATCCGGTCTTCATGTCCCGCACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATAAACAGTGCGCAGCAACAACCAACCCTGCATCTTCCTGCCTCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCa                                                              >  1:1088472/1‑149 (MQ=255)
                                                                                   ccAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCAGCCGGCCCCa                                                              >  2:848737/1‑149 (MQ=255)
                                                                                     aGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCCTCTTCATGCATCTGGTTGGTGCGGATTTGGATCTCAACGGATTGTCCCCCCGGCCCCCGa                                                            >  2:80310/1‑149 (MQ=255)
                                                                                          aacccggcTTCGTGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATACTGACAGTGCGCAGCAACACCCAACTCTGCATCTTCATTCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCAc                                                       <  1:385638/142‑1 (MQ=255)
                                                                                           ttcGGTCTTCATGTCGCGACCGCGCGCCGGCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCCACGGTTTTTCCACCCGGCCCCAACACCACg                                                      <  2:12158/147‑1 (MQ=255)
                                                                                                       gTCCCGCACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGAc                                          <  2:197022/149‑1 (MQ=255)
                                                                                                       gTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGAc                                          <  1:729417/149‑1 (MQ=255)
                                                                                                        tCCCGAAAGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAGCACCCAACTCTGCATCTTCATGAATCTGTTTGGTGCGGATGTGGATCTCAACGGTATTTCCACCCGGCTCCAGAACCACGGTATGAATAGACt                                         >  1:1052281/1‑149 (MQ=255)
                                                                                                          ccGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCACAGAACCACGGTATGAATAGACTGa                                       >  1:1047607/1‑149 (MQ=255)
                                                                                                              aCGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAAc                                   <  2:964173/149‑1 (MQ=255)
                                                                                                                  gcgcCGCCAGCAGCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGtt                               <  2:989034/149‑1 (MQ=255)
                                                                                                                         cagcagCCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTc                        >  1:911076/1‑149 (MQ=255)
                                                                                                                          agcagcCGCGCCCTCTTTATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCg                       >  2:413098/1‑149 (MQ=255)
                                                                                                                                   gctcttgttATAGTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGa              <  2:913656/142‑1 (MQ=255)
                                                                                                                                   gcCCTCCTTATATTTACAGTGCGCAGCAACACCCAACTCTGCAGCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGTTTTCGGGTTAGCGa              <  1:690406/149‑1 (MQ=255)
                                                                                                                                    cccTTTTGATATTCGCAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGAc             <  2:888966/149‑1 (MQ=255)
                                                                                                                                         tttATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATaa                                    >  2:427855/1‑121 (MQ=255)
                                                                                                                                         tttATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATaa                                    <  1:427855/121‑1 (MQ=255)
                                                                                                                                          ttATATTTACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATc       >  1:753065/1‑149 (MQ=255)
                                                                                                                                               tttACAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATCGTCaa  >  2:342984/1‑149 (MQ=255)
                                                                                                                                               tttACAGTGAGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACACGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGAAGTAATctccaa  <  2:481609/149‑6 (MQ=255)
                                                                                                                                                  |                                                                                                                                                 
TCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCTTCCTGCCACGCAATCAGTTTACGCAGCCAGGCAATCCGGTCTTCATGTCCCGAACGTGCGCCGCCAGCAGCCGCGCCCTCTTTATATTTCCAGTGCGCAGCAACACCCAACTCTGCATCTTCATGCATCTGTTTGGTGCGGATTTGGATCTCAACGGTTTTTCCACCCGGCCCCAGAACCACGGTATGAATAGACTGATAACCGTTTGGTTTCGGGTTAGCGACGTAATCGTCAA  >  NC_000913_3_pae_tpiA/2912441‑2912732

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A