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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,929,007 A→G 45.6% G71G (GGT→GGC)  araE ← arabinose transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,929,0070AG45.6% 11.2 / 75.2 90G71G (GGT→GGC) araEarabinose transporter
Reads supporting (aligned to +/- strand):  ref base A (18/31);  new base G (16/25);  total (34/56)
Fisher's exact test for biased strand distribution p-value = 8.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.12e-01

TCAGGCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGTA  >  minE/1928943‑1929070
                                                                |                                                               
tCAGGCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCg                                                              >  1:1153996/1‑68 (MQ=255)
tCAGGCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCg                                                              >  1:2151584/1‑68 (MQ=255)
 cAGGCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAg                                                            <  1:3333284/69‑1 (MQ=255)
    gCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTTCACCGAGcat                                                         <  1:2981956/69‑1 (MQ=255)
    gCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGcat                                                         <  1:1134632/69‑1 (MQ=255)
    gCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGcat                                                         <  1:2964878/69‑1 (MQ=255)
    gCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGcat                                                         <  1:1241484/69‑1 (MQ=255)
    gCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGcat                                                         <  1:3355619/69‑1 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:1093911/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:2896041/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:1888247/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:181460/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:468686/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:508821/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:527824/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:1595697/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:686978/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:957757/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:136187/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:944377/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:757178/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:837190/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatcat                                                      >  1:128093/1‑68 (MQ=255)
        tATTTACGCCCCAGGCGGAACGACAGCCACCCATTAAACAGCGCACCAATTGCTGCGCCGAGcatca                                                       >  1:306461/1‑67 (MQ=255)
          tttACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGct                                                   >  1:2603850/1‑69 (MQ=255)
          tttACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGct                                                   >  1:2235604/1‑69 (MQ=255)
               gCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGctacta                                               <  1:1894453/68‑1 (MQ=255)
               gCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGctacta                                               <  1:2248145/68‑1 (MQ=255)
               gCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGctacta                                               <  1:3015761/68‑1 (MQ=255)
               gCCCCAAGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGctacta                                               <  1:1038370/68‑1 (MQ=255)
                    aGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAaccacc                                         <  1:2261302/69‑1 (MQ=255)
                    aGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAaccacc                                         <  1:1735517/69‑1 (MQ=255)
                        ggAACGACAGCCAACCATTAAACATCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:1491775/69‑1 (MQ=255)
                        ggAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:2119802/69‑1 (MQ=255)
                        ggAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:56734/69‑1 (MQ=255)
                        ggAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:2093225/69‑1 (MQ=255)
                        ggAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:1306000/69‑1 (MQ=255)
                        ggAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:3359233/69‑1 (MQ=255)
                         gAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCAtt                                     <  1:1147135/68‑1 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCAGCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:3105075/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:3372090/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:565649/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:412144/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:2958494/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:982376/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:2410457/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:2168191/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:2099901/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:1963927/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:1303575/1‑68 (MQ=255)
                           aCGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTcc                                   >  1:1509524/1‑68 (MQ=255)
                                 gCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAAc                            <  1:482499/69‑1 (MQ=255)
                                 gCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAAc                            <  1:873127/69‑1 (MQ=255)
                                 gCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAAc                            <  1:1271820/69‑1 (MQ=255)
                                 gCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAAc                            <  1:3337498/69‑1 (MQ=255)
                                              cAGCGCACCAATTGCTGCACCGAGCATCATGctact                                                >  1:126273/1‑36 (MQ=255)
                                                  gcACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAAc                            <  1:46934/52‑1 (MQ=255)
                                                          tgctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:3238177/69‑1 (MQ=255)
                                                          tgctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:369071/69‑1 (MQ=255)
                                                          tgctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:1760449/69‑1 (MQ=255)
                                                          tgctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:554162/69‑1 (MQ=255)
                                                          tgctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:3149818/69‑1 (MQ=255)
                                                          tgctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:249560/69‑1 (MQ=255)
                                                           gctgcGCTGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1175462/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:364553/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:567487/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1635150/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:768056/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:536391/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:829947/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1780909/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1147534/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:3302481/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:2728365/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:295597/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:3006476/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:2098905/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1964066/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:3292748/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1795875/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1963219/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1888982/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1848792/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:3415397/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:2657808/69‑1 (MQ=255)
                                                           gctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1832728/69‑1 (MQ=255)
                                                           gctgcACCGAGCATCATTCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   >  1:389104/1‑68 (MQ=255)
                                                           gctgcACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGt   <  1:2234144/68‑1 (MQ=255)
                                                            ctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:1609108/68‑1 (MQ=255)
                                                            ctgcGCCGAGCATCATGCTACTGACCACCCATTCCTGCAAACGGCTGGTCAGCACAAAGTGATCGGTa  <  1:2879986/68‑1 (MQ=255)
                                                                |                                                               
TCAGGCTGTATTTACGCCCCAGGCGGAACGACAGCCAACCATTAAACAGCGCACCAATTGCTGCACCGAGCATCATGCTACTAACCACCCATTCCTGCAAACGACTGGTCAGCACAAAGTGATCGGTA  >  minE/1928943‑1929070

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