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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,315,024 C→T 37.2% D213N (GAC→AAC)  alsA ← fused D‑allose transporter subunits and ATP‑binding components of ABC superfamily

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,315,0240CT37.2% 75.7 / 82.8 78D213N (GAC→AAC) alsAfused D‑allose transporter subunits and ATP‑binding components of ABC superfamily
Reads supporting (aligned to +/- strand):  ref base C (23/26);  new base T (11/18);  total (34/44)
Fisher's exact test for biased strand distribution p-value = 4.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.52e-01

GTCATTTGACACATCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTACGCAACT  >  W3110S.gb/4314956‑4315092
                                                                    |                                                                    
gTCATTTGACACATCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCg                                                                     >  1:4190653/1‑70 (MQ=255)
   aTTTGACACATCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCaaa                                                                 <  1:4502569/71‑1 (MQ=255)
   aTTTGACACATCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCaaa                                                                 <  1:2592975/71‑1 (MQ=255)
   aTTTGACACATCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCaa                                                                  <  1:3828097/70‑1 (MQ=255)
         cacaTCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGc                                                           >  1:3146316/1‑71 (MQ=255)
            aTCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGaa                                                        >  1:4659668/1‑71 (MQ=255)
               gCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAAtt                                                      <  1:1551547/70‑1 (MQ=255)
               gCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAAtt                                                      <  1:360499/70‑1 (MQ=255)
                cTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTc                                                    <  1:3359521/71‑1 (MQ=255)
                 ttACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCa                                                                   <  1:253379/55‑1 (MQ=255)
                  tACTATGCCGCTGCAAAGGCTGCTGCCGTCTTTCATCACCGTATAGCGGTc                                                                      >  1:3539264/1‑51 (MQ=255)
                  tACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTc                                                                      >  1:3722027/1‑51 (MQ=255)
                  tACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCg                                                  >  1:2870136/1‑71 (MQ=255)
                    cTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCg                                                          <  1:3999199/61‑1 (MQ=255)
                    cTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCg                                                          <  1:366963/61‑1 (MQ=255)
                     tATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCa                                                                   <  1:4002221/51‑1 (MQ=255)
                     tATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCa                                                                   <  1:1347143/51‑1 (MQ=255)
                      aTGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCaa                                              >  1:740296/1‑71 (MQ=255)
                      aTGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCaa                                              >  1:4851526/1‑71 (MQ=255)
                       tGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAAc                                             >  1:3269276/1‑71 (MQ=255)
                        gCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACt                                            >  1:4073757/1‑71 (MQ=255)
                         ccGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACtt                                           <  1:4866374/71‑1 (MQ=255)
                         ccGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACtt                                           <  1:1779482/71‑1 (MQ=255)
                         ccGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACt                                            <  1:226814/70‑1 (MQ=255)
                         ccGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACt                                            <  1:4883502/70‑1 (MQ=255)
                         ccGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACt                                            <  1:2933137/70‑1 (MQ=255)
                         ccGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACtt                                           <  1:5047699/71‑1 (MQ=255)
                                 aaCGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGc                                       >  1:4567961/1‑67 (MQ=255)
                                  aCGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGa                                                         >  1:1828607/1‑48 (MQ=255)
                                  aCGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGc                                                 >  1:2826735/1‑56 (MQ=255)
                                  aCGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCgaga                                   >  1:4893665/1‑70 (MQ=255)
                                  aCGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGat                                  <  1:770176/71‑1 (MQ=255)
                                   cGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGata                                 <  1:3128912/71‑1 (MQ=255)
                                   cGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGata                                 <  1:2827193/71‑1 (MQ=255)
                                       gctgcCGTCTTTCATCACCGTATAGCGGTTGCaaa                                                                 <  1:2883864/35‑1 (MQ=255)
                                       gctgcCGTCTTTCATCACCCTATAGCGGTCGCAAATACGGCGAATTTCCGCCa                                               >  1:3938359/1‑53 (MQ=255)
                                        ctgcCGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGAc                            <  1:3652921/71‑1 (MQ=255)
                                        ctgcCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGAc                            <  1:5092246/71‑1 (MQ=255)
                                           ccGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACtt                                           <  1:4298377/53‑1 (MQ=255)
                                           ccGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACg                           <  1:3565143/69‑1 (MQ=255)
                                           ccGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGa                          <  1:1568795/70‑1 (MQ=255)
                                           ccGTCTTTCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGa                          <  1:3987794/70‑1 (MQ=255)
                                             gTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCgag                                    >  1:130791/1‑58 (MQ=255)
                                             gTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACGTATGCgag                                    >  1:387334/1‑58 (MQ=255)
                                              tCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGc                                       <  1:1039853/54‑1 (MQ=255)
                                                tttCATCACCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGata                                 >  1:4005025/1‑58 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGTGAATTTCCGCCAACt                                            <  1:78713/47‑1 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAAttt                                                     >  1:5101891/1‑38 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAAt                                                       >  1:37633/1‑36 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGc                                                 >  1:4036225/1‑42 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACt                                            <  1:1816966/47‑1 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTa                                          >  1:1803304/1‑49 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATg                                        >  1:1980928/1‑51 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGc                                       <  1:4698511/52‑1 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGa                          >  1:3922502/1‑65 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATg                        >  1:3783899/1‑67 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCg                    >  1:861574/1‑71 (MQ=255)
                                                tttCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCg                    >  1:1050931/1‑71 (MQ=255)
                                                   catcaCCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGt                   <  1:4077947/69‑1 (MQ=255)
                                                    atcaCCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACtt                                           >  1:2176071/1‑44 (MQ=255)
                                                     tcaCCGTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACg                           <  1:3622388/59‑1 (MQ=255)
                                                       aCCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCctc             >  1:3147114/1‑71 (MQ=255)
                                                        ccGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCctct            >  1:1250254/1‑71 (MQ=255)
                                                         cGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCtt           <  1:4615998/71‑1 (MQ=255)
                                                         cGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGCCCGTACCCTCtt           <  1:3028500/71‑1 (MQ=255)
                                                          gTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACGCTCttt          <  1:661869/71‑1 (MQ=255)
                                                          gTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCttt          <  1:1972120/71‑1 (MQ=255)
                                                          gTATAGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCttt          <  1:4096995/71‑1 (MQ=255)
                                                           tataGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTa         >  1:4279335/1‑71 (MQ=255)
                                                           tataGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTa         >  1:4263539/1‑71 (MQ=255)
                                                           tataGCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTa         >  1:456778/1‑71 (MQ=255)
                                                           tataGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTa         <  1:2919553/71‑1 (MQ=255)
                                                             taGCGGTTGCAAATACGGCGAATTTCCGCCAACTTa                                          >  1:3245369/1‑36 (MQ=255)
                                                               gCGGTTGCAAATACGGCGAATTTCCGCCAACTTAt                                         >  1:3742320/1‑35 (MQ=255)
                                                               gCGGTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTACGc      <  1:2190630/70‑1 (MQ=255)
                                                               gCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAg                              <  1:1785648/46‑1 (MQ=255)
                                                               gCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAg                              <  1:1779752/46‑1 (MQ=255)
                                                                 ggTTGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTACGCAAc   >  1:4708750/1‑71 (MQ=255)
                                                                 ggTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTACGCAAc   <  1:181291/71‑1 (MQ=255)
                                                                  gTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTACGCAACt  <  1:4821323/71‑1 (MQ=255)
                                                                    |                                                                    
GTCATTTGACACATCGCTTACTATGCCGCTGCAAACGCTGCTGCCGTCTTTCATCACCGTATAGCGGTCGCAAATACGGCGAATTTCCGCCAACTTATGCGAGATATAGACGATGGCCGTACCCTCTTTACGCAACT  >  W3110S.gb/4314956‑4315092

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