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 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,642,062 +T coding (208/213 nt) cspF → Qin prophage; cold shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,642,0591.T95.7% 161.4 / 0.7 47coding (205/213 nt)cspFQin prophage; cold shock protein
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base T (24/21);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 2.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTG  >  NC_000913/1641960‑1642154
                                                                                                    |                                                                                                
gcgcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTAcc                                                                                                   <  2:44834/100‑1 (MQ=255)
gcgcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTAcc                                                                                                   <  2:604731/100‑1 (MQ=255)
 cgcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t                                                                                                 >  2:1125904/1‑100 (MQ=255)
  gcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑t                                                                                               >  1:563259/1‑100 (MQ=255)
  gcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑t                                                                                               >  1:12573/1‑100 (MQ=255)
   cTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tt                                                                                              <  2:872239/100‑1 (MQ=255)
   cTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tt                                                                                              >  2:378674/1‑100 (MQ=255)
     cAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttc                                                                                            >  2:1019152/1‑98 (MQ=255)
     cAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttc                                                                                            >  2:209683/1‑98 (MQ=255)
     cAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttc                                                                                            <  2:636424/100‑3 (MQ=255)
      aaTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttca                                                                                           <  1:81190/100‑4 (MQ=255)
      aaTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttca                                                                                           >  2:572067/1‑97 (MQ=255)
          tcCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAg                                                                                        <  2:367906/100‑1 (MQ=255)
           ccGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGc                                                                                       >  1:411595/1‑100 (MQ=255)
           ccGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGc                                                                                       <  1:719099/100‑1 (MQ=255)
            cgcgATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCt                                                                                      >  1:64793/1‑100 (MQ=255)
             gcgATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCta                                                                                     >  1:42996/1‑100 (MQ=255)
                   cAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTaa                                                                               >  2:17005/1‑100 (MQ=255)
                     gaagaaATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAg                                                                             >  1:1001138/1‑100 (MQ=255)
                     gaagaaATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAg                                                                             >  1:1116210/1‑100 (MQ=255)
                      aagaaATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑TGTTCATGAGCTATATTAAAGc                                                                            <  1:1226367/100‑1 (MQ=255)
                         aaaTTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCttt                                                                         <  1:267169/100‑1 (MQ=255)
                            ttACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAAt                                                                      >  2:739737/1‑100 (MQ=255)
                                   cGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGc                                                               <  2:1004781/100‑1 (MQ=255)
                                     gATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGccc                                                             >  1:103970/1‑100 (MQ=255)
                                      aTTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGcccc                                                            >  1:865931/1‑100 (MQ=255)
                                           gcgTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCg                                                        <  2:453043/99‑1 (MQ=255)
                                            cgTGGAATTTTGTCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGa                                                      >  1:856891/1‑100 (MQ=255)
                                             gTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCTGGCCCCATCGGAt                                                     >  2:821441/1‑100 (MQ=255)
                                              tGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATc                                                    >  2:526613/1‑100 (MQ=255)
                                              tGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATc                                                    <  2:935885/100‑1 (MQ=255)
                                                  aTTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATcacac                                                <  2:462576/100‑1 (MQ=255)
                                                   ttttGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATcacaca                                               <  1:866051/100‑1 (MQ=255)
                                                      tGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATgg                                            <  1:915681/100‑1 (MQ=255)
                                                        ccGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGgag                                          <  1:964476/100‑1 (MQ=255)
                                                             tAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGttt                                     <  1:54826/100‑1 (MQ=255)
                                                               aaTGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGttttt                                   <  1:1125914/100‑1 (MQ=255)
                                                                aTGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTa                                  >  1:816998/1‑100 (MQ=255)
                                                                 tGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTAt                                 >  1:419165/1‑100 (MQ=255)
                                                                  ggTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATg                                <  1:395531/100‑1 (MQ=255)
                                                                    tCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGaa                              >  1:185172/1‑100 (MQ=255)
                                                                         gTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCATGCCCCATCGGATCACACATGGAGAGATTTTATTAATAAcc                         >  2:161970/1‑100 (MQ=255)
                                                                         gTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAAcc                         <  1:739742/100‑1 (MQ=255)
                                                                            gCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCg                      <  2:411591/100‑1 (MQ=255)
                                                                            gCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCg                      >  1:228550/1‑100 (MQ=255)
                                                                              ccTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtc                    >  1:669352/1‑100 (MQ=255)
                                                                              ccTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtc                    <  1:17005/100‑1 (MQ=255)
                                                                                ttCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtctg                  <  2:865925/100‑1 (MQ=255)
                                                                                  cAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtctgtc                >  2:667068/1‑100 (MQ=255)
                                                                                       gCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgat           <  2:164277/100‑1 (MQ=255)
                                                                                       gCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtg             >  1:272491/1‑98 (MQ=255)
                                                                                        ccAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgatg          >  1:206951/1‑100 (MQ=255)
                                                                                        ccAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgatg          >  1:1205441/1‑100 (MQ=255)
                                                                                        ccAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgatg          <  2:228548/100‑1 (MQ=255)
                                                                                         cAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgatga         >  2:316779/1‑100 (MQ=255)
                                                                                            tGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTTAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGAc        >  2:482844/1‑98 (MQ=255)
                                                                                              tttACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGt    <  1:242413/100‑1 (MQ=255)
                                                                                               ttACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGtt   <  1:1224375/100‑1 (MQ=255)
                                                                                               tcaCC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTg  <  2:792273/98‑1 (MQ=255)
                                                                                                    |                                                                                                
GCGCTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTG  >  NC_000913/1641960‑1642154

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A