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
A3 F50 I2 R1 257 49.9 1554294 99.0% 1538751 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,311,736 G→A intergenic (‑52/+97) rpsO ← / ← truB 30S ribosomal subunit protein S15/tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,311,7360GA98.0% 175.5 / NA 49intergenic (‑52/+97)rpsO/truB30S ribosomal subunit protein S15/tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (26/22);  minor base C (1/0);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGCAGTGCTACCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCGATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAGGCGCAACGCGGCC  >  NC_000913/3311589‑3311877
                                                                                                                                                   |                                                                                                                                             
cagcagTGCTACCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATc                                                                                                                                            >  2:667283/1‑151 (MQ=255)
 agcagTGCTACCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATcc                                                                                                                                           >  1:637615/1‑151 (MQ=255)
  gcagTGCTACCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATccc                                                                                                                                          >  2:709487/1‑151 (MQ=255)
       gCTACCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAgtgt                                                                                                                                     <  2:505387/151‑1 (MQ=255)
          aCCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTa                                                                                                                                    <  2:14216/149‑1 (MQ=255)
          aCCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTAc                                                                                                                                   <  1:219645/150‑1 (MQ=255)
          aCCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTAc                                                                                                                                   <  2:505684/150‑1 (MQ=255)
           ccTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGt                                                                                                                                 >  2:672374/1‑151 (MQ=255)
              gAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTAc                                                                                                                              <  2:170453/151‑1 (MQ=255)
               aaCTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACg                                                                                                                             >  1:519715/1‑151 (MQ=255)
               aaCTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACg                                                                                                                             <  1:771389/151‑1 (MQ=255)
                      gTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAgtg                                                                                                                      >  2:408542/1‑151 (MQ=255)
                      gTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAgtg                                                                                                                      <  2:335577/151‑1 (MQ=255)
                        aGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTTCGCAAAgtgt                                                                                                                     <  2:635504/150‑1 (MQ=255)
                        aGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGtt                                                                                                                    >  1:610945/1‑151 (MQ=255)
                                                  cAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGc                                                                                          <  2:719450/151‑1 (MQ=255)
                                                      cTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGt                                                                                       >  2:716373/1‑150 (MQ=255)
                                                        cAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTa                                                                                      >  1:303755/1‑149 (MQ=255)
                                                         aGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTc                                                                                   >  2:523703/1‑151 (MQ=255)
                                                          gAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCt                                                                                  >  2:111362/1‑151 (MQ=255)
                                                                      gCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGAc                                                                      >  2:45900/1‑151 (MQ=255)
                                                                         gTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTg                                                                   >  2:775803/1‑151 (MQ=255)
                                                                         gTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTg                                                                   >  1:55077/1‑151 (MQ=255)
                                                                           tGCTTCAGTACTTAGAGACATTGTAAAACTCCACAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAAACCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGCTAAGCGGCAGTATTCTACTCGTAGAGACCTgct                                                                 >  1:308676/1‑149 (MQ=255)
                                                                              ttCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATc                                                              >  1:737911/1‑151 (MQ=255)
                                                                               tCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATc                                                              <  1:76639/150‑1 (MQ=255)
                                                                                cAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCg                                                             <  2:526774/150‑1 (MQ=255)
                                                                                 aGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGc                                                            >  2:449405/1‑150 (MQ=255)
                                                                                 aGTACTTAGAGACATTATAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCAACCTGTTATCGCa                                                           <  2:68669/151‑1 (MQ=255)
                                                                                      ttAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACg                                                      >  1:356647/1‑151 (MQ=255)
                                                                                       tAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAAGACGCCGCTCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACgg                                                     >  2:238030/1‑151 (MQ=255)
                                                                                                 ttAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTa                                            <  1:606460/150‑1 (MQ=255)
                                                                                                  tAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACg                                          >  2:548156/1‑151 (MQ=255)
                                                                                                   aaaaCTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACg                                          <  2:381988/150‑1 (MQ=255)
                                                                                                      aCTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCgg                                      <  1:57503/151‑1 (MQ=255)
                                                                                                        tCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGAAGGTTAACATTACGCCGGGt                                    >  2:491520/1‑151 (MQ=255)
                                                                                                           aaaGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTAtt                                 <  2:228168/151‑1 (MQ=255)
                                                                                                              gTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCa                               <  1:56827/150‑1 (MQ=255)
                                                                                                              gTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCa                               >  2:56858/1‑150 (MQ=255)
                                                                                                                   taGAATGAAAGGACGCCGGTCTCTAATTCGGTCATCCCAGTGTATGTTACGCAAAGGGTTAAACAATTTACGCGACGTTAAGCGGAGGTATTCTAATCGTGTCGACCTGTTATCGCAAGTGGGTTAACATTATGCCGGGTATTCAaccacc                         >  1:741630/1‑151 (MQ=255)
                                                                                                                     gAATGAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAg                       <  2:230718/151‑1 (MQ=255)
                                                                                                                         gAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGcg                    <  2:427778/150‑1 (MQ=255)
                                                                                                                         gAAAGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGcg                    >  1:414209/1‑150 (MQ=255)
                                                                                                                          aaaGGACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGcgac                  <  2:668278/151‑1 (MQ=255)
                                                                                                                             ggACGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAg               <  2:693683/151‑1 (MQ=255)
                                                                                                                               aCGCCGATCTCTAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAGgc             >  1:308682/1‑151 (MQ=255)
                                                                                                                                        tctAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAGGCGCAACGCgg    >  1:432828/1‑151 (MQ=255)
                                                                                                                                         ctAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAGGCGCAAcgc      <  2:247745/148‑1 (MQ=255)
                                                                                                                                          tAATTCAGCAATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAGGCGCAACGCGGcc  >  1:552045/1‑151 (MQ=255)
                                                                                                                                                   |                                                                                                                                             
CAGCAGTGCTACCTGAACTTCGGTAGAACCGGTGTCGTTTGCGTCACGACCAAACTCAGAAACGATTTTAGCTGTTGCTTCAGTACTTAGAGACATTTTAAAACTCCAAAGTATATAGAATGAAAGGACGCCGATCTCTAATTCAGCGATCCCAGTGTACGTTACGCAAAGTGTTAAACAATTTACGCGACGTTAAGCGGCAGTATTCTACTCGTAGCGACCTGTTATCGCAAGACGGTTAACATTACGCCGGGTATTCAACCACCAGGCGACGAGGCGCAACGCGGCC  >  NC_000913/3311589‑3311877

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A