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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,673,345 (T)7→8 coding (157/366 nt) mdtJ ← multidrug efflux system transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,673,3381.T100.0% 169.2 / NA 54I55N (ATC→AAC) mdtJmultidrug efflux system transporter
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (26/28);  total (26/28)

TCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑TTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGC  >  NC_000913/1673207‑1673471
                                                                                                                                    |                                                                                                                                     
tCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑ttttttt                                                                                                                                >  1:873957/1‑139 (MQ=255)
tCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑ttttttt                                                                                                                                >  2:966740/1‑139 (MQ=255)
tCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑ttttttt                                                                                                                                >  1:399174/1‑139 (MQ=255)
           aGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGaaa                                                                                                                      <  2:723675/139‑1 (MQ=255)
               tggtTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAagaga                                                                                                                  <  1:966740/139‑1 (MQ=255)
                  ttAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGaa                                                                                                               <  2:970970/139‑1 (MQ=255)
                  ttAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGaa                                                                                                               <  2:151451/139‑1 (MQ=255)
                        cGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑ttttttttaa                                                                                                                             >  1:753906/1‑115 (MQ=255)
                        cGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑ttttttttaa                                                                                                                             <  2:753906/118‑4 (MQ=255)
                         ggCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAAtatata                                                                                                        <  2:151581/139‑1 (MQ=255)
                                        cGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAatcat                                                                                         >  2:978599/1‑139 (MQ=255)
                                            aaaCTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCAcc                                                                                     <  1:676692/139‑1 (MQ=255)
                                                  tcgtcgAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGaa                                                                                                               >  2:1107/1‑107 (MQ=255)
                                                  tcgtcgAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGaa                                                                                                               <  1:1107/107‑1 (MQ=255)
                                                  tcgtcgAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCAtt                                                                               >  1:924504/1‑139 (MQ=255)
                                                              aaaaCGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgccg                                                                   <  2:924504/139‑1 (MQ=255)
                                                                aaggCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgccgcc                                                                 <  2:873957/136‑1 (MQ=255)
                                                                   gCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCAtt                                                              <  2:610973/139‑1 (MQ=255)
                                                                       aaCAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgc                                                                     >  2:505190/1‑128 (MQ=255)
                                                                       aaCAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgc                                                                     <  1:505190/128‑1 (MQ=255)
                                                                                 taaataaaATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGACGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGc                                                >  2:1105199/1‑139 (MQ=255)
                                                                                   aataaaataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTc                                              <  2:671269/139‑1 (MQ=255)
                                                                                      aaaataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCGTTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGcc                                           >  1:1251084/1‑139 (MQ=255)
                                                                                       aaataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGccc                                          <  2:155347/139‑1 (MQ=255)
                                                                                       aaataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGccc                                          >  1:1037355/1‑139 (MQ=255)
                                                                                       aaataCCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGccc                                          >  2:908170/1‑139 (MQ=255)
                                                                                               aTACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCAtt                                  >  1:176186/1‑139 (MQ=255)
                                                                                                  ccTTCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGAc                               <  1:978599/139‑1 (MQ=255)
                                                                                                     tCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCt                                               >  1:329043/1‑120 (MQ=255)
                                                                                                     tCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCt                                               <  2:329043/120‑1 (MQ=255)
                                                                                                     tCCCACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGc                            >  1:1146118/1‑139 (MQ=255)
                                                                                                      cccACAGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCg                           >  2:311380/1‑139 (MQ=255)
                                                                                                          caGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACg                                                 >  1:1176176/1‑113 (MQ=255)
                                                                                                          caGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACg                                                 <  2:1176176/113‑1 (MQ=255)
                                                                                                          caGCGCATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTAcc                       >  1:1007795/1‑139 (MQ=255)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCg                                                                                                                         >  1:795823/1‑38 (MQ=25)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCg                                                                                                                         <  2:795823/38‑1 (MQ=25)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCg                                                                                                                         <  1:1178021/38‑1 (MQ=25)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCg                                                                                                                         >  2:1178021/1‑38 (MQ=25)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAaga                                                                                                                    <  1:69099/43‑1 (MQ=37)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAaga                                                                                                                    >  2:69099/1‑43 (MQ=37)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgccgcc                                                                 >  2:818733/1‑94 (MQ=255)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAgccgcc                                                                 <  1:818733/94‑1 (MQ=255)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGt                    >  1:542880/1‑139 (MQ=255)
                                                                                                             cgcATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGt                    >  2:968091/1‑139 (MQ=255)
                                                                                                               cATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACaga                                                                                                 >  2:86630/1‑60 (MQ=39)
                                                                                                               cATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACaga                                                                                                 <  1:86630/60‑1 (MQ=39)
                                                                                                               cATAAGCTACGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTaa                  >  1:330008/1‑139 (MQ=255)
                                                                                                                       aCGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGaa                                                                                                               <  2:915836/38‑1 (MQ=25)
                                                                                                                       aCGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGaa                                                                                                               >  1:915836/1‑38 (MQ=25)
                                                                                                                       aCGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGActcaggcaggct                                       >  2:791753/1‑99 (MQ=255)
                                                                                                                       aCGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGActcaggcaggct                                       <  1:791753/110‑12 (MQ=255)
                                                                                                                       aCGCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTa          <  1:362388/139‑1 (MQ=255)
                                                                                                                         gCCTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGc        <  2:542880/139‑1 (MQ=255)
                                                                                                                          ccTAAGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCa       <  2:123554/139‑1 (MQ=255)
                                                                                                                              aGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAg   >  1:549112/1‑139 (MQ=255)
                                                                                                                              aGGCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAg   >  1:942708/1‑139 (MQ=255)
                                                                                                                               ggCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCGTTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGc  <  2:1251084/139‑1 (MQ=255)
                                                                                                                               ggCGATTTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGc  <  1:311380/139‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                     
TCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCATCAGCGATAAACTTTCGTCGAATAACAAAACGCTAAACAAGGTAATAAATAAAATACCGATACCTTCCCACAGCGCATAAGCTACGCCTAAGGCGA‑TTTTTTTAACGGCGAAAGAGAGAAATATATACGACAGAGAAATCATCACCAGCATTAAAATAAAGCCGCCATTTCCCTCACTGACGCTCGCCCATTTCATTGACAGCGTACCGGTAATTTCTGTAGCAATAGC  >  NC_000913/1673207‑1673471

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A