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
A14 F1 I1 R1 770 68.5 3470224 91.7% 3182195 103.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,400,348 G→A P476S (CCC→TCC)  abgT ← p‑aminobenzoyl‑glutamate transporter, membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,400,3480GA90.0% 151.4 / 9.1 61P476S (CCC→TCC) abgTp‑aminobenzoyl‑glutamate transporter, membrane protein
Reads supporting (aligned to +/- strand):  ref base G (3/3);  new base A (26/28);  total (30/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01

TCAAGTAATCTCAGCATCCGTTCTCTCTTAAGACAAACGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATACGGATGAGTCGGCAATACGAA  >  NC_000913/1400220‑1400473
                                                                                                                                |                                                                                                                             
tcAAGTAATCTCAGCATCCGTTCTCTCTTAAGACAAACGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAAc                                                                                                                     <  1:1334538/139‑1 (MQ=255)
         ctcAGCATCCGTTCTCTCTTAAGACAAACGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATagtaa                                                                                                            <  2:1625850/139‑1 (MQ=255)
                tCCGTTCTCTCTTAAGACAAACGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCa                                                                                                     >  2:1538777/1‑139 (MQ=255)
                                   aaCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAggg                                                                                                                               >  2:708137/1‑94 (MQ=255)
                                   aaCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAggg                                                                                                                               <  1:708137/94‑1 (MQ=255)
                                   aaCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTa                                                                                                                       >  1:1040775/1‑102 (MQ=255)
                                   aaCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTc                                                                                           <  2:567080/130‑1 (MQ=255)
                                   aaCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTc                                                                                           >  1:567080/1‑130 (MQ=255)
                                   aaCGGGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGAcca                                                                                                                       <  2:1040775/102‑3 (MQ=255)
                                    aCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGTCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAg                                                                                 <  2:1382492/139‑1 (MQ=255)
                                    aCGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAg                                                                                 <  2:947074/139‑1 (MQ=255)
                                         ggTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTAccc                                                                                                      >  1:22290/1‑113 (MQ=255)
                                         ggTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTAccc                                                                                                      <  2:22290/113‑1 (MQ=255)
                                         ggTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTg                                                                            >  2:60542/1‑139 (MQ=255)
                                            aaaTACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAg                                                                         <  1:24709/139‑1 (MQ=255)
                                            aaaTACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAg                                                                         <  1:60542/139‑1 (MQ=255)
                                                aCCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAAt                                                                     >  1:1650833/1‑139 (MQ=255)
                                                   cGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTAc                                                                                                        >  1:510109/1‑101 (MQ=255)
                                                   cGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTAc                                                                                                        <  2:510109/101‑1 (MQ=255)
                                                    ggACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGttt                                                                                                 <  2:924723/107‑1 (MQ=255)
                                                    ggACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGttt                                                                                                 >  1:924723/1‑107 (MQ=255)
                                                    ggACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCaa                                                                 >  1:807787/1‑139 (MQ=255)
                                                          aTCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACaa                                                                                                                            <  1:383988/74‑1 (MQ=255)
                                                          aTCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACaa                                                                                                                            >  2:383988/1‑74 (MQ=255)
                                                          aTCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGa                                                               <  2:88963/135‑1 (MQ=255)
                                                          aTCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGa                                                               >  1:88963/1‑135 (MQ=255)
                                                          aTCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACa                                                           >  1:1094253/1‑139 (MQ=255)
                                                           tCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAg                                                          >  2:514150/1‑139 (MQ=255)
                                                           tCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGaaa                                                             <  2:596685/136‑1 (MQ=255)
                                                           tCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGaaa                                                             >  1:596685/1‑136 (MQ=255)
                                                           tCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAg                                                          <  2:196358/139‑1 (MQ=255)
                                                                 gACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAAc                                                                                                                     <  1:1412658/74‑1 (MQ=255)
                                                                 gACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAAc                                                                                                                     >  2:1412658/1‑74 (MQ=255)
                                                                       cAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAgg                                              >  2:418167/1‑139 (MQ=255)
                                                                                 cGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGaaa                                                             <  1:1633637/114‑1 (MQ=255)
                                                                                 cGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGaaa                                                             >  2:1633637/1‑114 (MQ=255)
                                                                                 cGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGgc                                    >  2:946759/1‑139 (MQ=255)
                                                                                 cGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACG‑ATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAg                                                          <  2:1662480/116‑1 (MQ=255)
                                                                                 cGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACG‑ATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAg                                                          >  1:1662480/1‑116 (MQ=255)
                                                                                  gCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACaa                                                                                                                            >  2:666126/1‑50 (MQ=255)
                                                                                  gCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACaa                                                                                                                            <  1:666126/50‑1 (MQ=255)
                                                                                  gCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACaa                                                  <  1:461947/124‑1 (MQ=255)
                                                                                  gCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACaa                                                  >  2:461947/1‑124 (MQ=255)
                                                                                    cAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCt                                 >  1:617226/1‑139 (MQ=255)
                                                                                    cAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCt                                 <  2:1094253/139‑1 (MQ=255)
                                                                                     aGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTa                                >  1:366458/1‑139 (MQ=255)
                                                                                     aGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTa                                <  1:514150/139‑1 (MQ=255)
                                                                                         aCATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAgg                            <  1:946759/139‑1 (MQ=255)
                                                                                            tCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCaa                         <  1:1538777/139‑1 (MQ=255)
                                                                                               gcagcCATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATAc                      <  2:1650833/139‑1 (MQ=255)
                                                                                                    cATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGt                                                                                            <  1:1385767/64‑1 (MQ=255)
                                                                                                    cATACCACCAAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGt                                                                                            >  2:1385767/1‑64 (MQ=255)
                                                                                                          accaAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATACGGATGAGTCgg           <  2:617226/139‑1 (MQ=255)
                                                                                                           ccaAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGt                                                                                            >  1:602802/1‑57 (MQ=255)
                                                                                                           ccaAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGt                                                                                            <  2:602802/57‑1 (MQ=255)
                                                                                                            caAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAg                                                                         <  2:1188358/75‑1 (MQ=255)
                                                                                                            caAAAAGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAg                                                                         >  1:1188358/1‑75 (MQ=255)
                                                                                                             aaaaaGATAAGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATACGGATGAGTCGGCaa        >  1:457264/1‑139 (MQ=255)
                                                                                                                   aTAAGTGGATAGGCCAAGACTGACGAATAGTACGTACCCAGTTTCGAGTCTGGTTTGTAGCGTTGAAGGCATCCTAGAAACAAAGGAACAAAAGGATATACCGGCGCTATAGGCAATACGGATCAGTCGCCAATACGaa  >  2:365232/1‑139 (MQ=255)
                                                                                                                      aGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGt                                                                                            <  2:1587313/46‑1 (MQ=255)
                                                                                                                      aGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGt                                                                                            >  1:1587313/1‑46 (MQ=255)
                                                                                                                      aGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCACGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATACGGAt                  >  2:247622/1‑120 (MQ=255)
                                                                                                                      aGTGGATAGGACAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATACGGAt                  <  1:247622/120‑1 (MQ=255)
                                                                                                                                |                                                                                                                             
TCAAGTAATCTCAGCATCCGTTCTCTCTTAAGACAAACGTGGGTAAATACCCGGACCTATCGGCAGACCGACAAGATACCACGCCAGCAACATCAGCAGCCATACCACCAAAAAGATAAGTGGATAGGGCAAGACTAACGAATAGTAAGTACCCAGTTTCGCGTCTGGTTTGTAGCGTTGCAGGAATCCAAGAAACAGTGGAACAAAAGGAGATACCGGCGCTAAAGGCAATACGGATGAGTCGGCAATACGAA  >  NC_000913/1400220‑1400473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A