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 1,284,125 C→A 43.4% A1968A (GCC→GCA)  yeeJ → adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,284,1250CA43.4% 73.7 / 131.4 138A1968A (GCC→GCA) yeeJadhesin
Reads supporting (aligned to +/- strand):  ref base C (42/36);  new base A (14/46);  total (56/82)
Fisher's exact test for biased strand distribution p-value = 4.24e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

Only 100 of 139 total aligned reads displayed.

TTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGCCGCCACCAACACTGATTTA  >  minE/1284059‑1284182
                                                                  |                                                         
gttCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                                         >  1:3119208/2‑69 (MQ=255)
    cATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                                         <  1:2397105/65‑1 (MQ=255)
    cATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                                         <  1:2792111/65‑1 (MQ=255)
       aaCGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCa                                                         <  1:1229057/62‑1 (MQ=255)
        aCGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCt                                                  >  1:1815947/1‑68 (MQ=255)
          ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                                               >  1:1090379/1‑69 (MQ=255)
          ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                                               >  1:1889943/1‑69 (MQ=255)
          ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                                               <  1:1263562/69‑1 (MQ=255)
          ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                                               >  1:841766/1‑69 (MQ=255)
          ggCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGc                                               >  1:1705178/1‑69 (MQ=255)
             gtcaCAATACAGACACAGATAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:2204535/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:601545/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:1193529/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:1834730/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:848103/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:1269158/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:2903242/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:3004057/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:1615067/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:3157958/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:3271160/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:852052/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:712021/66‑1 (MQ=255)
             gtcaCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCttt                                            <  1:523499/66‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:242513/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:2451561/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:2547147/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:2587025/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:2261118/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:980217/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:81608/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:3066497/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:309375/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:788609/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:3308477/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:45563/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:522026/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:1575628/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:1652571/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:1942884/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:1196447/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:1983894/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATc                                         <  1:1993847/69‑1 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATc                                         >  1:1924680/1‑69 (MQ=255)
                aCAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATc                                         >  1:786642/1‑69 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTTGCAACTCAAGCACCGCCCATGTT‑CTAGCttt                                            <  1:3044072/59‑1 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                                            <  1:1304132/60‑1 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                                            <  1:380671/60‑1 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                                            <  1:3383530/60‑1 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCttt                                            <  1:1705196/60‑1 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                                     >  1:3209583/1‑67 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                                     >  1:3119245/1‑67 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                                     >  1:1556537/1‑67 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                                     >  1:2410764/1‑67 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                                     >  1:280502/1‑67 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTg                                     >  1:502280/1‑67 (MQ=255)
                      cagacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCCAGCttt                                            <  1:435191/60‑1 (MQ=255)
                        gacacagacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATcc                                 <  1:801326/69‑1 (MQ=255)
                              gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc                           >  1:1734703/1‑69 (MQ=255)
                              gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc                           >  1:2070052/1‑69 (MQ=255)
                              gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc                           >  1:1432185/1‑69 (MQ=255)
                              gacaACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGAc                           >  1:959548/1‑69 (MQ=255)
                              gacaACCGTCAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGa                            >  1:2198153/1‑68 (MQ=255)
                                caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa                         >  1:317396/1‑69 (MQ=255)
                                caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa                         >  1:1617245/1‑69 (MQ=255)
                                caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa                         >  1:2739252/1‑69 (MQ=255)
                                caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa                         >  1:2735281/1‑69 (MQ=255)
                                caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa                         >  1:1398825/1‑69 (MQ=255)
                                caACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTa                         >  1:2238324/1‑69 (MQ=255)
                                  aCCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATc                       <  1:1026425/69‑1 (MQ=255)
                                  aCCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATc                       <  1:2478479/69‑1 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:3171438/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:1386683/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:1171693/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:515708/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:201990/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:1301504/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:3096995/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:790081/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:1447427/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATcc                                 >  1:1326864/1‑58 (MQ=255)
                                   ccGTGAAGGTTACTGGCAACCCAAGCACCGCACATGTTGCTAGCTTTATCGCTGATc                                  >  1:3370054/1‑57 (MQ=255)
                                   ccGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATc                       <  1:2623362/68‑1 (MQ=255)
                                    cGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATcgc                     >  1:1545416/1‑69 (MQ=255)
                                                        cAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATGCATCGACTATcgcc                    >  1:2296132/1‑50 (MQ=255)
                                                        cAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGCCGCCACCAACACTGAttt   >  1:468070/1‑67 (MQ=255)
                                                        cAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGCCGCCACCAACACTGATTTa  >  1:2205039/1‑68 (MQ=255)
                                                        cAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGCCGCCACCAACACTGATTTa  >  1:2074335/1‑68 (MQ=255)
                                                        cAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGCCGCCACCAACACTGATTTa  >  1:2810397/1‑68 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:1357799/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:514510/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:3052421/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:3092821/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:1957232/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:404826/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:361887/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:3384233/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:3334347/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:149500/40‑1 (MQ=255)
                                                            cACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACt                          <  1:1498521/40‑1 (MQ=255)
                                                                  |                                                         
TTTCCATAACGGCGTAACAATACAGACACAGACAACCGTGAAAGTCACTGGCAACTCAAGCACCGCCCATGTTGCTAGCTTTATCGCTGATCCATCGACTATCGCCGCCACCAACACTGATTTA  >  minE/1284059‑1284182

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