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
A7 F1 I2 R1 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 573,440 C→T R24C (CGC→TGC)  rusA → DLP12 prophage, endonuclease RUS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913573,4400CT100.0% 185.2 / NA 54R24C (CGC→TGC) rusADLP12 prophage, endonuclease RUS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (29/25);  total (29/25)

AGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGATCGCCGTCGCC  >  NC_000913/573305‑573575
                                                                                                                                       |                                                                                                                                       
aGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGtgca                                                                                                                                      >  2:22588/1‑139 (MQ=255)
          cTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAg                                                                                                                            <  1:698260/139‑1 (MQ=255)
                ggTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCaga                                                                                                                      <  1:588120/139‑1 (MQ=255)
                     ggCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGggc                                                                                                                 >  1:813597/1‑139 (MQ=255)
                           aaCACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCAt                                                                                                           >  2:600040/1‑139 (MQ=255)
                            acacAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATa                                                                                                          >  1:1343273/1‑139 (MQ=255)
                             cacaGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATAc                                                                                                         <  2:1392914/139‑1 (MQ=255)
                                     aTCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATaa                                                                                                 >  2:1037742/1‑139 (MQ=255)
                                            tGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCGCGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGcc                                                                                          >  1:1159472/1‑139 (MQ=255)
                                            tGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGcc                                                                                          >  2:273192/1‑139 (MQ=255)
                                               aaGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGa                                                                                       <  1:600040/139‑1 (MQ=255)
                                                    ggggTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCAt                                                                                  >  1:1355188/1‑139 (MQ=255)
                                                              aGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCa                                                                        <  1:60809/139‑1 (MQ=255)
                                                              aGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCa                                                                        <  2:1343273/139‑1 (MQ=255)
                                                                gCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgggg                                                                                                                  >  1:784261/1‑95 (MQ=255)
                                                                gCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgggg                                                                                                                  <  2:784261/95‑1 (MQ=255)
                                                                 cGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATg                                                                     >  2:12654/1‑139 (MQ=255)
                                                                     aaTACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTgg                                                                 >  2:1240428/1‑139 (MQ=255)
                                                                             cAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  1:1037742/139‑1 (MQ=255)
                                                                             cAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  1:1240428/139‑1 (MQ=255)
                                                                             cAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  2:813597/139‑1 (MQ=255)
                                                                              aGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          >  1:151481/1‑121 (MQ=255)
                                                                              aGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          <  2:151481/121‑1 (MQ=255)
                                                                               gCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCt                                                       >  1:43594/1‑139 (MQ=255)
                                                                                   cacaTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATAc                                                                                                         <  1:996174/85‑1 (MQ=255)
                                                                                   cacaTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGata                                                              >  1:162507/1‑128 (MQ=255)
                                                                                   cacaTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGata                                                              <  2:162507/128‑1 (MQ=255)
                                                                                   cacaTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGACATAATCGCGGGTGCATGCACGTCAGCGCAGAGGGGCAGGCATAc                                                                                                         >  2:996174/1‑85 (MQ=255)
                                                                                     caTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          <  1:113243/114‑1 (MQ=255)
                                                                                     caTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          >  2:113243/1‑114 (MQ=255)
                                                                                          cccTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTATAAACGCa                                                                        >  1:653972/1‑111 (MQ=255)
                                                                                          cccTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTATAAACGCa                                                                        <  2:653972/111‑1 (MQ=255)
                                                                                               gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGtgcacg                                                                                                                                    <  2:938744/46‑1 (MQ=255)
                                                                                               gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGtgcacg                                                                                                                                    >  1:938744/1‑46 (MQ=255)
                                                                                               gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAAGGCTGGATATCGGCCTGGCTTTGCCTGTGaaa                                       >  2:960938/1‑139 (MQ=255)
                                                                                                ccTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGaaaa                                      >  1:506925/1‑139 (MQ=255)
                                                                                                    cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         >  1:1108654/1‑116 (MQ=255)
                                                                                                    cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGc                                                         <  2:1108654/116‑1 (MQ=255)
                                                                                                    cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCg                                  >  1:896301/1‑139 (MQ=255)
                                                                                                    cGAGCAATAATCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCg                                  >  1:1223227/1‑139 (MQ=255)
                                                                                                           taatCGCTATTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAg                           <  1:12654/139‑1 (MQ=255)
                                                                                                                 gtaatagcGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGaa                                        >  1:76254/8‑120 (MQ=255)
                                                                                                                 gtaatagcGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGaa                                        <  2:76254/113‑1 (MQ=255)
                                                                                                                   aTTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgggg                                                                                                                  >  1:969213/1‑44 (MQ=255)
                                                                                                                   aTTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAgggg                                                                                                                  <  2:969213/44‑1 (MQ=255)
                                                                                                                   aTTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCa                                                                        <  2:193955/86‑1 (MQ=255)
                                                                                                                   aTTACCGCCATAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCa                                                                        >  1:193955/1‑86 (MQ=255)
                                                                                                                            aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          <  2:668629/75‑1 (MQ=255)
                                                                                                                            aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                                                          >  1:668629/1‑75 (MQ=255)
                                                                                                                            aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATg                                                                     >  1:165929/1‑80 (MQ=255)
                                                                                                                            aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATg                                                                     <  2:165929/80‑1 (MQ=255)
                                                                                                                            aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGatat                                                             <  2:960548/88‑1 (MQ=255)
                                                                                                                            aTAATCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGatat                                                             >  1:960548/1‑88 (MQ=255)
                                                                                                                              aaTCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCAt                               <  2:1088741/116‑1 (MQ=255)
                                                                                                                              aaTCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCAt                               >  1:1088741/1‑116 (MQ=255)
                                                                                                                              aaTCGCGGGTGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGAtcgcc        >  1:730626/1‑139 (MQ=255)
                                                                                                                                    gggTGCACGCGCGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGAtcgccgtcgcc  <  2:1159472/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
AGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTGAGTGCCACATGCCGGATCGCCGTCGCC  >  NC_000913/573305‑573575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A