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 193 39.9 1341687 91.8% 1231668 149.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,586,424 C→T R113H (CGC→CAC)  hsdR ← endonuclease R Type I restriction enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,586,4240CT100.0% 154.8 / NA 41R113H (CGC→CAC) hsdRendonuclease R Type I restriction enzyme
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/21);  total (20/21)

TTTCTCGCACCTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAAGGCGATTTTGCCGAGTTCACGCAGG  >  NC_000913/4586281‑4586567
                                                                                                                                               |                                                                                                                                               
tttCTCGCACCTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAAcc                                                                                                                                           <  1:455635/150‑1 (MQ=255)
     cGCACCTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAg                                                                                                                                       <  1:474275/149‑1 (MQ=255)
        aCCTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCa                                                                                                                                  <  2:229788/151‑1 (MQ=255)
        aCCTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCa                                                                                                                                  <  1:51299/151‑1 (MQ=255)
         ccTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGc                                                                                                                                   >  2:105593/1‑149 (MQ=255)
          ctgctgTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAgg                                                                                                                                >  2:271372/1‑151 (MQ=255)
               gTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGcaca                                                                                                                            <  2:252981/150‑1 (MQ=255)
                    aGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTggg                                                                                                                      >  2:531805/1‑151 (MQ=255)
                        gttgttTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCAt                                                                                                                   <  2:531957/150‑1 (MQ=255)
                          tgttTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCg                                                                                                                 <  1:269836/150‑1 (MQ=255)
                            ttttAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTg                                                                                                              >  2:365532/1‑151 (MQ=255)
                             tttAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTg                                                                                                              <  1:175146/150‑1 (MQ=255)
                              ttAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTg                                                                                                              >  1:552869/1‑149 (MQ=255)
                                aGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTg                                                                                                              >  2:591840/1‑147 (MQ=255)
                                 gCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATc                                                                                                         <  1:661438/151‑1 (MQ=255)
                                  cGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCg                                                                                                        <  2:121590/151‑1 (MQ=255)
                                        cACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATg                                                                                                   >  2:161960/1‑150 (MQ=255)
                                                ggTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTg                                                                                          <  1:241987/151‑1 (MQ=255)
                                                      agagGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGc                                                                                    <  2:242166/151‑1 (MQ=255)
                                                        agGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCt                                                                                  <  2:199368/151‑1 (MQ=255)
                                                                   acGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATg                                                                       >  1:611211/1‑151 (MQ=255)
                                                                    cGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATgc                                                                      <  2:317690/151‑1 (MQ=255)
                                                                     gTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATgcg                                                                     >  1:58403/1‑151 (MQ=255)
                                                                                acaAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTtgt                                                          >  2:8605/1‑151 (MQ=255)
                                                                                  aaaCACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTtgtg                                                         >  2:142523/1‑150 (MQ=255)
                                                                                     caccggcaccggGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAAt                                                     <  2:44089/151‑1 (MQ=255)
                                                                                      accggcaccggGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAAt                                                     >  1:400304/1‑150 (MQ=255)
                                                                                             ccggGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACagag                                               >  2:625383/1‑149 (MQ=255)
                                                                                                ggAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAt                                          >  1:47900/1‑151 (MQ=255)
                                                                                                ggAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAt                                          >  2:647362/1‑151 (MQ=255)
                                                                                                   aGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAtgtt                                       <  2:632927/151‑1 (MQ=255)
                                                                                                      cATAATCTTTAGTGACCAAACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGAtgttgt                                     <  1:576153/150‑1 (MQ=255)
                                                                                                        tAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGtcat                                  >  2:266857/1‑151 (MQ=255)
                                                                                                         aaTCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGtcatc                                 >  2:630854/1‑151 (MQ=255)
                                                                                                           tCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGtcatca                                >  1:459173/1‑150 (MQ=255)
                                                                                                              ttAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGtcatca                                <  1:105590/147‑1 (MQ=255)
                                                                                                              ttAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGtcatca                                <  1:462337/147‑1 (MQ=255)
                                                                                                              ttAGTGACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATcaaca                             <  2:583101/150‑1 (MQ=255)
                                                                                                                   gACCAGACGGTAGTACCAGACAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAAGGCg                       <  2:78667/151‑1 (MQ=255)
                                                                                                                                       cAGCCAGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAAGGCGATTTTGCCGAGTTCACGc     >  1:203259/1‑149 (MQ=255)
                                                                                                                                            aGGTGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAAGGCGATTTTGCCGAGTTCACGCAgg  >  2:167889/1‑147 (MQ=255)
                                                                                                                                               |                                                                                                                                               
TTTCTCGCACCTGCTGTTCAAGCTGTTGTTTTAGCGTCAGCACTTCCTGGTGATAGAGGTTTTCACCACGTTCCGGCAACACAAACACCGGCACCGGGAAGTCATAATCTTTAGTGACCAGACGGTAGTACCAGACAGCCAGGCGGAACCCGAGTCGCAGGCACATCTGGGCATCGTTGAGATCGTTATGATATTCGTGCACCGCCTGGTTACCAATGCGGCGTAATTTGTGAAATACAGAGAGGATGTTGTCATCAACAAAGGCGATTTTGCCGAGTTCACGCAGG  >  NC_000913/4586281‑4586567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A