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
A8 F1 I1 R1 771 44.8 2153074 94.1% 2026042 109.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,641,403 A→G V51A (GTT→GCT)  cspB ← Qin prophage, cold shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,641,4030AG100.0% 216.1 / NA 62V51A (GTT→GCT) cspBQin prophage, cold shock protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (33/29);  total (33/29)

TGTCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAACCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACC  >  NC_000913/1641277‑1641536
                                                                                                                              |                                                                                                                                     
tGTCCGTATCTCTACTCAGGGATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGAccat                                                                                                                           >  2:631316/1‑137 (MQ=255)
tGTCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCtt                                                                                                                           >  1:382323/1‑139 (MQ=255)
  tCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCtttt                                                                                                                                 >  2:388882/1‑131 (MQ=255)
  tCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCtttt                                                                                                                                 <  1:388882/131‑1 (MQ=255)
  tCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCa                                                                                                                         >  2:1060855/1‑139 (MQ=255)
  tCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTCTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCa                                                                                                                         >  2:439462/1‑139 (MQ=255)
          tctACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGt                                                                                                                 <  2:382323/139‑1 (MQ=255)
            tACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATa                                                                                                                     >  1:173907/1‑133 (MQ=255)
            tACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATa                                                                                                                     <  2:173907/133‑1 (MQ=255)
               tCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTCTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGAt                                                                                                            <  1:439462/139‑1 (MQ=255)
                   gCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTAAGCCCCACTCTCTATAGAGAAGGTAGCCTTTCGACCTTAAAATAAGGTTCGTAAAtt                                                                                                        >  1:500210/1‑139 (MQ=255)
                    cATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTa                                                                                                       <  1:803985/139‑1 (MQ=255)
                      tCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGtt                                                                                                                >  1:185506/1‑128 (MQ=255)
                      tCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGtt                                                                                                                <  2:185506/128‑1 (MQ=255)
                                           taCAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGaa                                                                                             >  1:15753/1‑126 (MQ=255)
                                           taCAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGaa                                                                                             <  2:15753/126‑1 (MQ=255)
                                                aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCtttt                                                                                                                                 <  1:340148/85‑1 (MQ=255)
                                                aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCtttt                                                                                                                                 >  2:340148/1‑85 (MQ=255)
                                                aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTg                                                                                                                                <  1:1009880/86‑1 (MQ=255)
                                                aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTg                                                                                                                                >  2:1009880/1‑86 (MQ=255)
                                                aCGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaa                                                                           >  1:740120/1‑139 (MQ=255)
                                                 cGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaaa                                                                          <  2:740120/139‑1 (MQ=255)
                                                   aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTa                                                                                                       <  1:230401/108‑1 (MQ=255)
                                                   aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTa                                                                                                       >  2:230401/1‑108 (MQ=255)
                                                   aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAaca                                                                        >  1:558563/1‑139 (MQ=255)
                                                   aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAaca                                                                        >  2:102980/1‑139 (MQ=255)
                                                   aGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAaca                                                                        >  1:720648/1‑139 (MQ=255)
                                                     cGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                       <  1:54105/138‑1 (MQ=255)
                                                     cGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                       >  2:54105/1‑138 (MQ=255)
                                                                      tAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAAc                                                     <  1:975758/139‑1 (MQ=255)
                                                                      tAATGATGACATTTGCTGCTGCAGGACCTTTAGCAACACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATTAAc                                                     >  2:758361/1‑139 (MQ=255)
                                                                           atgaCATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGtt                                                                                                                >  2:245884/1‑75 (MQ=255)
                                                                           atgaCATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGtt                                                                                                                <  1:245884/75‑1 (MQ=255)
                                                                                      tgctgcCAGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                     <  2:500210/139‑1 (MQ=255)
                                                                                      tgctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                     <  1:1060855/139‑1 (MQ=255)
                                                                                       gctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGa                                    <  1:583956/139‑1 (MQ=255)
                                                                                        ctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGaaa                                                                                    <  2:742201/90‑1 (MQ=255)
                                                                                        ctgcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGaaa                                                                                    >  1:742201/1‑90 (MQ=255)
                                                                                          gcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGc                                                                               >  2:741847/1‑93 (MQ=255)
                                                                                          gcAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGc                                                                               <  1:741847/93‑1 (MQ=255)
                                                                                                ccTTTAGCACCACTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTAt                           >  1:405011/1‑139 (MQ=255)
                                                                                                        accacTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTAcc                                                           <  1:481567/99‑1 (MQ=255)
                                                                                                        accacTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTAcc                                                           >  2:481567/1‑99 (MQ=255)
                                                                                                           acTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaaa                                                                          >  1:276015/1‑81 (MQ=255)
                                                                                                           acTCTCTATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACaaa                                                                          <  2:276015/81‑1 (MQ=255)
                                                                                                             tctctATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCa              <  1:102980/139‑1 (MQ=255)
                                                                                                               tctATAGAGAAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCAtt            >  2:708051/1‑139 (MQ=255)
                                                                                                                       gaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTta                                                                >  1:946219/1‑79 (MQ=255)
                                                                                                                       gaAGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTta                                                                <  2:946219/79‑1 (MQ=255)
                                                                                                                        aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGaaaaa                                                                                  >  1:803902/1‑60 (MQ=255)
                                                                                                                        aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGaaaaa                                                                                  <  2:803902/60‑1 (MQ=255)
                                                                                                                        aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                       >  1:499825/1‑71 (MQ=255)
                                                                                                                        aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAacac                                                                       <  2:499825/71‑1 (MQ=255)
                                                                                                                        aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAAcaca                                                                      >  2:99353/1‑72 (MQ=255)
                                                                                                                        aaGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAAcaca                                                                      <  1:99353/72‑1 (MQ=255)
                                                                                                                         aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAATTAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAcc  >  2:438670/1‑139 (MQ=255)
                                                                                                                         aGGTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAcc  >  2:311879/1‑139 (MQ=255)
                                                                                                                           gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGcaca                                                                            <  2:1017211/63‑1 (MQ=255)
                                                                                                                           gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCaa                                                      <  2:428969/85‑1 (MQ=255)
                                                                                                                           gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                     >  2:1014539/1‑102 (MQ=255)
                                                                                                                           gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCg                                     <  1:1014539/102‑1 (MQ=255)
                                                                                                                           gTAGCCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCAt             >  1:485357/1‑126 (MQ=255)
                                                                                                                              |                                                                                                                                     
TGTCCGTATCTCTACTCAGGCATCAGCCTTCTTCGTTATCGTATACAGACGAGCGATGAATTTTAATCAGTAATGATGACATTTGCTGCTGCAGGACCTTTAGCACCACTCTCTATAGAGAAGGTAACCTTTTGACCTTCAAATAAGGTTCGATAATTATCATTCTGAATCGCAGAAAAATGCACAAACACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAACC  >  NC_000913/1641277‑1641536

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