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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,458,921 T→C 13.7% K6K (AAA→AAG)  nusG ← transcription termination factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,458,9210TC13.7% 128.1 / 13.5 51K6K (AAA→AAG) nusGtranscription termination factor
Reads supporting (aligned to +/- strand):  ref base T (20/24);  new base C (4/3);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 6.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

ATGCTCACGCAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGAATACCATC  >  W3110S.gb/3458852‑3458990
                                                                     |                                                                     
atGCTCACGCAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCtttt                                                                      >  1:1937981/1‑71 (MQ=255)
  gCTCACGCAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCtttt                                                                      >  1:2736813/1‑69 (MQ=255)
   cTCACGCAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCtttt                                                                      <  1:4111785/68‑1 (MQ=255)
   cTCACGCAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAg                                                                   <  1:2199785/71‑1 (MQ=255)
         cAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCtt                                                             <  1:1088162/71‑1 (MQ=255)
         cAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCtt                                                             <  1:4174209/71‑1 (MQ=255)
          aGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCtt                                                             >  1:2383455/1‑70 (MQ=255)
          aGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTCTTAGGAGCTTc                                                            <  1:1802759/71‑1 (MQ=255)
             gACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTCTTAGGAGCTTCAGa                                                         >  1:2021695/1‑71 (MQ=255)
              aCGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTa                                                                    <  1:2142826/59‑1 (MQ=255)
               cGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAg                                                          >  1:3967818/1‑68 (MQ=255)
                 ttGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCttttt                                                                     <  1:4057170/55‑1 (MQ=255)
                 ttGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACa                                                       <  1:2200804/69‑1 (MQ=255)
                   gCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACAtct                                                    >  1:3334920/1‑70 (MQ=255)
                   gCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTCTTAGGAGCTTCAGACAtct                                                    <  1:2554253/70‑1 (MQ=255)
                     tACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCttt                                                                       >  1:1643589/1‑49 (MQ=255)
                        gcgGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAAc                                              <  1:3078403/71‑1 (MQ=255)
                             cTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAg                                                                   <  1:2603601/45‑1 (MQ=255)
                             cTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACAt                                                      <  1:4045785/58‑1 (MQ=255)
                             cTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAg                                                 <  1:4172144/63‑1 (MQ=255)
                             cTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAg                                         <  1:3954427/71‑1 (MQ=255)
                               tCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGc                                                               >  1:4366803/1‑47 (MQ=255)
                               tCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCt                                            <  1:868834/66‑1 (MQ=255)
                                cAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCa                                                           >  1:2294400/1‑50 (MQ=255)
                                cAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACAtctc                                                   >  1:341332/1‑58 (MQ=255)
                                cAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCa                                                  >  1:886357/1‑59 (MQ=255)
                                cAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGc                                       >  1:2435274/1‑70 (MQ=255)
                                 aaaaCCGGAAAACGCCTGAACGACGTACCAGCGCTTCTTAGGAGCTTCAGACATCTCAGAACCTCAGGc                                       >  1:3306151/1‑69 (MQ=255)
                                  aaaCCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTa                                                                    >  1:3609024/1‑39 (MQ=255)
                                  aaaCCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACAt                                                      <  1:568812/53‑1 (MQ=255)
                                  aaaCCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAg                                    <  1:3390113/71‑1 (MQ=255)
                                   aaCCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCt                                                              <  1:402457/44‑1 (MQ=255)
                                   aaCCGGAAAACGCCTGAACGACGTACCAGCGCTTCTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGt                                   <  1:4058230/71‑1 (MQ=255)
                                    aCCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGt                                   >  1:1797637/1‑70 (MQ=255)
                                      cGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGAt                                <  1:2727220/71‑1 (MQ=255)
                                       ggAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTc                                           >  1:530000/1‑59 (MQ=255)
                                       ggAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATa                               <  1:1231367/71‑1 (MQ=255)
                                        gAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATa                               >  1:1384795/1‑70 (MQ=255)
                                          aaaCGCCTGAACGACGTACCAGCGCTTTTTAGGAGCtt                                                             <  1:2886015/38‑1 (MQ=255)
                                          aaaCGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAg                            >  1:3149040/1‑71 (MQ=255)
                                          aaaCGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACATCAGGCCAGTGATAAAg                            <  1:79474/71‑1 (MQ=255)
                                           aaCGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAg                            >  1:82007/1‑70 (MQ=255)
                                               ccTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATAc                       >  1:321555/1‑71 (MQ=255)
                                                cTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATAcc                      <  1:1063934/71‑1 (MQ=255)
                                                  gAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAg                    >  1:3552022/1‑71 (MQ=255)
                                                   aaCGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCa                     <  1:17811/69‑1 (MQ=255)
                                                    acgacgTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGc                  <  1:2593070/71‑1 (MQ=255)
                                                    acgacgTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGc                  <  1:4038577/71‑1 (MQ=255)
                                                    acgacgTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGc                  >  1:749837/1‑71 (MQ=255)
                                                      gacgTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAg                                         >  1:63682/1‑46 (MQ=255)
                                                        cgTACCAGCGCTTCTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAAc              >  1:948618/1‑71 (MQ=255)
                                                               gcgcTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATAcc                      <  1:2589351/56‑1 (MQ=255)
                                                               gcgcTTCTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGAATa       >  1:4502981/1‑71 (MQ=255)
                                                                cgcTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGAATAc      <  1:453473/71‑1 (MQ=255)
                                                                 gcTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGaa               >  1:667837/1‑61 (MQ=255)
                                                                  cTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGaa         >  1:4041921/1‑66 (MQ=255)
                                                                   tttttAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCa                     >  1:1852015/1‑53 (MQ=255)
                                                                     tttAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGAATACCAt   <  1:2110969/69‑1 (MQ=255)
                                                                     tttAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGAATACCATc  >  1:3185228/1‑70 (MQ=255)
                                                                     tttAGGAGCTTCAGACATCTCAGAACATCAGGCCAGTGATAAAGGATAACAGGCGAACCAGaa         >  1:3056412/1‑63 (MQ=255)
                                                                     |                                                                     
ATGCTCACGCAGCGACGTTGCTACGCGGCCTTCAAAACCGGAAAACGCCTGAACGACGTACCAGCGCTTTTTAGGAGCTTCAGACATCTCAGAACCTCAGGCCAGTGATAAAGGATACCAGGCGAACCAGAATACCATC  >  W3110S.gb/3458852‑3458990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A