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 2,771,105 G→A 11.5% N79N (AAC→AAT)  ypjL ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,771,1050GA11.5% 227.5 / 16.9 79N79N (AAC→AAT) ypjLpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (33/36);  new base A (5/4);  total (39/40)
Fisher's exact test for biased strand distribution p-value = 7.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

CTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGT  >  W3110S.gb/2771036‑2771172
                                                                     |                                                                   
ctctTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGt                                                                    <  1:4002396/71‑1 (MQ=255)
 tctTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGtt                                                                   >  1:3593592/1‑71 (MQ=255)
  ctTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGtt                                                                   >  1:2587377/1‑70 (MQ=255)
   tttGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTg                                                                     <  1:2833688/67‑1 (MQ=255)
   tttGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtca                                                                 >  1:2168328/1‑71 (MQ=255)
    ttGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtcat                                                                >  1:3186349/1‑71 (MQ=255)
     tGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtc                                                                  <  1:1982758/68‑1 (MQ=255)
       acgacgCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCAc                                                             <  1:874039/71‑1 (MQ=255)
          acgCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtga                                                          <  1:355920/71‑1 (MQ=255)
           cgCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgat                                                         >  1:2230304/1‑71 (MQ=255)
            gCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgatg                                                        <  1:2858130/71‑1 (MQ=255)
            gCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgat                                                         >  1:1732626/1‑70 (MQ=255)
             ccAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgat                                                         >  1:877228/1‑69 (MQ=255)
             ccAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgat                                                         >  1:1019030/1‑69 (MQ=255)
             ccAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtg                                                           <  1:1995833/67‑1 (MQ=255)
              cAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATgag                                                      <  1:2832436/71‑1 (MQ=255)
              cAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATgag                                                      <  1:2607104/71‑1 (MQ=255)
               aGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTTATgaga                                                     <  1:2983871/71‑1 (MQ=255)
                gTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATgagag                                                    <  1:556129/71‑1 (MQ=255)
                 tCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGt                                                                    <  1:254249/54‑1 (MQ=255)
                   gCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGaaa                                                 >  1:756191/1‑71 (MQ=255)
                    ccGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAAt                                                <  1:4090573/71‑1 (MQ=255)
                    ccGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAAt                                                >  1:1900548/1‑71 (MQ=255)
                     cGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATg                                               >  1:4247226/1‑71 (MQ=255)
                      gTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACt                                                            <  1:3801876/57‑1 (MQ=255)
                       tACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGt                                                                    >  1:1886239/1‑48 (MQ=255)
                         cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATgagaga                                                   <  1:670960/63‑1 (MQ=255)
                         cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGt                                           <  1:3610936/71‑1 (MQ=255)
                         cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCg                                            >  1:1527386/1‑70 (MQ=255)
                           cccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTc                                          >  1:2789991/1‑70 (MQ=255)
                            ccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtca                                                                 >  1:1175161/1‑46 (MQ=255)
                            ccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGaa                                                  >  1:3764774/1‑61 (MQ=255)
                            ccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTc                                          <  1:4564597/69‑1 (MQ=255)
                              gTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtca                                                                 <  1:2613098/44‑1 (MQ=255)
                               tCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTg                                                                     >  1:2723829/1‑39 (MQ=255)
                                cAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtcatc                                                               >  1:427385/1‑44 (MQ=255)
                                 aaTCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtcat                                                                >  1:4592754/1‑42 (MQ=255)
                                 aaTCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtcat                                                                >  1:4383062/1‑42 (MQ=255)
                                 aaTCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtcat                                                                >  1:4597855/1‑42 (MQ=255)
                                 aaTCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgatga                                                       >  1:401205/1‑51 (MQ=255)
                                 aaTCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGc                                   <  1:2321843/71‑1 (MQ=255)
                                 aaTCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGc                                   >  1:3838383/1‑71 (MQ=255)
                                  aTCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGcc                                  <  1:4481008/71‑1 (MQ=255)
                                   tCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATgaga                                                     <  1:456215/51‑1 (MQ=255)
                                   tCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATg                                               <  1:2142033/57‑1 (MQ=255)
                                   tCGACAGCGCACCAATCAGCACCGTCGGAATATTGTTCATCACtgatg                                                        >  1:277467/1‑48 (MQ=255)
                                   acGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgatg                                                        >  1:2624588/2‑48 (MQ=255)
                                    cGACAGCGCACCAATCATCACCGTCGGCATATTCTtcatga                                                              >  1:1790366/1‑39 (MQ=21)
                                     gACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGt                               >  1:3439728/1‑71 (MQ=255)
                                     gACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGt                               >  1:3440329/1‑71 (MQ=255)
                                       cAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGc                                              >  1:1660854/1‑54 (MQ=255)
                                        aGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGaa                                                  >  1:3795644/1‑49 (MQ=255)
                                         gcgcACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCg                           <  1:2201650/71‑1 (MQ=255)
                                             aCCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATg                                               <  1:2260809/47‑1 (MQ=255)
                                             aCCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCaaga                                      <  1:1131495/56‑1 (MQ=255)
                                             aCCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACg                       <  1:251628/71‑1 (MQ=255)
                                             aCCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACg                       <  1:2795452/71‑1 (MQ=255)
                                             aCCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGAGCCGAACg                       <  1:3356136/71‑1 (MQ=255)
                                               cAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGt                                           <  1:4452322/49‑1 (MQ=255)
                                                 aTCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTca                    >  1:2816371/1‑69 (MQ=255)
                                                  tCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCaa                                        <  1:4493800/49‑1 (MQ=255)
                                                  tCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCt                  <  1:2395710/71‑1 (MQ=255)
                                                   cAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTg                 >  1:4016876/1‑71 (MQ=255)
                                                    aGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGc                >  1:2251193/1‑71 (MQ=255)
                                                    aGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGc                >  1:3783117/1‑71 (MQ=255)
                                                    aGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGc                >  1:369185/1‑71 (MQ=255)
                                                    aGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGc                >  1:374664/1‑71 (MQ=255)
                                                       aCCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCa             >  1:4602089/1‑71 (MQ=255)
                                                         cGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATa           <  1:1044727/71‑1 (MQ=255)
                                                         cGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATa           <  1:3795593/71‑1 (MQ=255)
                                                         cGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATa           <  1:3790198/71‑1 (MQ=255)
                                                          gTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATaa          <  1:3941305/71‑1 (MQ=255)
                                                             ggCATATTGTTAATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTc                     >  1:4392519/1‑57 (MQ=255)
                                                              gCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAAccc       <  1:1348416/70‑1 (MQ=255)
                                                               cATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGc                                   <  1:322189/41‑1 (MQ=255)
                                                                 tatTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGcc                                  <  1:608587/40‑1 (MQ=255)
                                                                 tatTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGcc                                  <  1:714404/40‑1 (MQ=255)
                                                                 tatTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTc                     <  1:1426359/53‑1 (MQ=255)
                                                                  atTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGt  >  1:1892031/1‑71 (MQ=255)
                                                                   ttGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCa             >  1:1723478/1‑59 (MQ=255)
                                                                   ttGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGt  <  1:2875266/70‑1 (MQ=255)
                                                                     |                                                                   
CTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGT  >  W3110S.gb/2771036‑2771172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A