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
A4 F195 I0 R2 483 52.1 1908604 98.1% 1872340 138.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,406,392 G→A 8.5% G68D (GGT→GAT)  nsrR → nitric oxide‑sensitive repressor for NO regulon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,406,3920GA 8.5% 141.7 / 4.5 47G68D (GGT→GAT) nsrRnitric oxide‑sensitive repressor for NO regulon
Reads supporting (aligned to +/- strand):  ref base G (22/21);  new base A (2/2);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.23e-01

ATTGCCAGAAGGGCGGATGACCAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCAAAGTTTTCTTA  >  NC_000913/4406246‑4406538
                                                                                                                                                  |                                                                                                                                                  
aTTGCCAGAAGGGCGGATGACCAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTa                                                                                                                                                  >  4:458004/1‑149 (MQ=255)
       gAAGGGCGGATGACCAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGc                                                                                                                                           >  3:195914/1‑149 (MQ=255)
           ggCGGATGACCAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGt                                                                                                                                       <  1:235749/149‑1 (MQ=255)
                 tGACCAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATa                                                                                                                                 <  3:370532/149‑1 (MQ=255)
                    ccAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGt                                                                                                                              >  4:331720/1‑149 (MQ=255)
                     cAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTa                                                                                                                             >  2:371816/1‑149 (MQ=255)
                        tATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTg                                                                                                                          >  3:167329/1‑149 (MQ=255)
                          tttCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGt                                                                                                                        >  3:214384/1‑149 (MQ=255)
                             cTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGAt                                                                                                                     <  4:432678/149‑1 (MQ=255)
                                aaGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGAtgtg                                                                                                                  <  1:106838/149‑1 (MQ=255)
                                  gTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATgtggt                                                                                                                <  1:381632/149‑1 (MQ=255)
                                  gTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATgtggt                                                                                                                >  2:160053/1‑149 (MQ=255)
                                               aCGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAg                                                                                                   <  4:214384/149‑1 (MQ=255)
                                                 ggCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGATAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGcc                                                                                                 >  1:195696/1‑149 (MQ=255)
                                                 ggCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGATAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGcc                                                                                                 >  3:169517/1‑149 (MQ=255)
                                                  gCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGccc                                                                                                <  3:458004/149‑1 (MQ=255)
                                                   cGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCt                                                                                               <  3:331720/149‑1 (MQ=255)
                                                       tcCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATc                                                                                           <  4:410947/149‑1 (MQ=255)
                                                         ccGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGc                                                                                         >  1:190343/1‑149 (MQ=255)
                                                          cGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCt                                                                                        <  2:270389/149‑1 (MQ=255)
                                                            tAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGATAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTgg                                                                                      <  2:195696/149‑1 (MQ=255)
                                                            tAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGATAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTgg                                                                                      <  4:169517/149‑1 (MQ=255)
                                                                      gTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTgcag                                                                            >  2:260013/1‑149 (MQ=255)
                                                                       tCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGaa                                                                                  >  4:149976/1‑142 (MQ=255)
                                                                       tCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGaa                                                                                  <  3:149976/142‑1 (MQ=255)
                                                                              aatcaatcAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGt                                                                    <  1:371816/149‑1 (MQ=255)
                                                                                tcaatcaaCTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGttt                                                                  >  4:465249/1‑149 (MQ=255)
                                                                                tcaatcaaCTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGttt                                                                  <  3:166993/149‑1 (MQ=255)
                                                                                   atcaaCTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGc                                                               >  4:385074/1‑149 (MQ=255)
                                                                                   atcaaCTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGc                                                               <  1:160053/149‑1 (MQ=255)
                                                                                   atcaaCTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGc                                                               >  3:140294/1‑149 (MQ=255)
                                                                                            gTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTaca                                                      <  1:237638/149‑1 (MQ=255)
                                                                                            gTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTaca                                                      <  4:195914/149‑1 (MQ=255)
                                                                                               gTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACAcct                                                   >  3:476287/1‑149 (MQ=255)
                                                                                                     gCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGt                                             >  1:80854/1‑149 (MQ=255)
                                                                                                               tgctgTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAAc                                   >  2:401361/1‑149 (MQ=255)
                                                                                                                 ctgTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAg                                 <  4:385889/149‑1 (MQ=255)
                                                                                                                    ttCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCa                              >  4:231386/1‑149 (MQ=255)
                                                                                                                       gTGGAAAAAATGGCGGCATTAGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACtt                           >  2:226912/1‑149 (MQ=255)
                                                                                                                         ggAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTc                         <  4:476287/149‑1 (MQ=255)
                                                                                                                          gAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCt                        >  2:41059/1‑149 (MQ=255)
                                                                                                                                       cATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCaaa           <  3:385074/149‑1 (MQ=255)
                                                                                                                                         ttCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCAAAGt         <  4:140294/149‑1 (MQ=255)
                                                                                                                                            gCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCAAAGtttt      >  3:118265/1‑149 (MQ=255)
                                                                                                                                              cTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGaa                                     >  4:165752/1‑116 (MQ=255)
                                                                                                                                              cTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGaa                                     <  3:165752/116‑1 (MQ=255)
                                                                                                                                               tGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCAAAGTTTTCtt   >  2:17243/1‑149 (MQ=255)
                                                                                                                                                gggTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCAAAGTTTTCTTa  >  1:256391/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
ATTGCCAGAAGGGCGGATGACCAGTATTTCTGAAGTGACTGACGTCTACGGCGTCTCCCGTAATCATATGGTCAAAATAATCAATCAACTTAGTCGTGCCGGCTACGTGACTGCTGTTCGTGGAAAAAATGGCGGCATTCGCCTGGGTAAACCGGCGAGTGCGATACGTATTGGTGATGTGGTGCGCGAGCTGGAGCCCTTATCGCTGGTGAATTGCAGCAGTGAGTTTTGCCACATTACACCTGCCTGTAGGTTGAAACAGGCACTTTCTAAGGCCGTGCAAAGTTTTCTTA  >  NC_000913/4406246‑4406538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A