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 2,407,200 A→G 37.9% D87D (GAT→GAC)  cyaA ← adenylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,407,2000AG37.9% 38.1 / 51.4 80D87D (GAT→GAC) cyaAadenylate cyclase
Reads supporting (aligned to +/- strand):  ref base A (35/14);  new base G (5/25);  total (41/39)
Fisher's exact test for biased strand distribution p-value = 2.30e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01

CTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAGGC  >  minE/2407139‑2407266
                                                             |                                                                  
cTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTa                                                             <  1:2355425/69‑1 (MQ=255)
cTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTa                                                             <  1:819472/69‑1 (MQ=255)
cTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTa                                                             <  1:2529529/69‑1 (MQ=255)
cTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTa                                                             <  1:373841/69‑1 (MQ=255)
cTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTa                                                             <  1:3227806/69‑1 (MQ=255)
cTACGGACGAGGTGCTGCCCATGGTGCATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTa                                                             <  1:685288/69‑1 (MQ=255)
             gctgcCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGTGGGTCCTGTACt                                                           >  1:3405658/1‑58 (MQ=255)
             gctgcCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGTGGGTCCTGTACTGACAt                                                      >  1:2609990/1‑63 (MQ=255)
             gctgcCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGTGGGTCCTGTACTGACATTCCAc                                                 >  1:2339698/1‑68 (MQ=255)
             gctgcCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGTGGGTCCTGTACTGACATTCCAc                                                 >  1:1734099/1‑68 (MQ=255)
             gctgcCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGTGGGTCCTGTACTGACATTCCAc                                                 >  1:3285691/1‑68 (MQ=255)
                       gtgtATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTc                                       >  1:1094998/1‑68 (MQ=255)
                       gtgtATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCa                                      >  1:3171129/1‑69 (MQ=255)
                       gtgtATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCa                                      >  1:301932/1‑69 (MQ=255)
                       gtgtATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCa                                      >  1:626740/1‑69 (MQ=255)
                       gtgtATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCa                                      >  1:1693418/1‑69 (MQ=255)
                       gtgtATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCa                                      >  1:2030297/1‑69 (MQ=255)
                       gtgtATACACCAGTAATCGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCa                                      >  1:92164/1‑69 (MQ=255)
                          tataCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGc                                   >  1:340564/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCt                                  >  1:1199586/1‑68 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTc                                 >  1:636611/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTc                                 >  1:263965/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTc                                 >  1:1583107/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTc                                 >  1:1830598/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTc                                 >  1:186990/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACCTTTCGGCAGATCCTGTACTGACATTCCACGATACAGTTCAAGCTc                                 >  1:211702/1‑69 (MQ=255)
                            taCACCAGTAATTGGAAGCTCACATTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTAAAGCTc                                 >  1:3351953/1‑69 (MQ=255)
                                    tAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGt                         <  1:3275221/69‑1 (MQ=255)
                                    tAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGt                         <  1:432052/69‑1 (MQ=255)
                                    tAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGt                         <  1:681471/69‑1 (MQ=255)
                                    tAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGt                         <  1:2001760/69‑1 (MQ=255)
                                    tAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGt                         <  1:465930/69‑1 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCa                                                  >  1:2602071/1‑43 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTa                        >  1:1512269/1‑69 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTa                        >  1:1322796/1‑69 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTa                        >  1:1216158/1‑69 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTa                        >  1:1573058/1‑69 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTa                        >  1:2659167/1‑69 (MQ=255)
                                     aaTTGGAAGCTCACCTTTCGGCGGATCCTCTACTGACATTCCACGATACAGTTCAAGCt                                  >  1:1586703/1‑59 (MQ=255)
                                      aTTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAg                       >  1:2886131/1‑69 (MQ=255)
                                        tGGAAGCTCACCTTTCGGCGGCTCCTGTACTGACATTCCCCGCTa                                             >  1:896462/1‑45 (MQ=255)
                                        tGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTg                     >  1:2125398/1‑69 (MQ=255)
                                        tGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTg                     >  1:977478/1‑69 (MQ=255)
                                         ggAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAgg                          >  1:2930474/1‑63 (MQ=255)
                                              cTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTg               <  1:1045212/69‑1 (MQ=255)
                                              cTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTg               <  1:2365836/69‑1 (MQ=255)
                                              cTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTg               <  1:347700/69‑1 (MQ=255)
                                                cACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAg             >  1:711539/1‑69 (MQ=255)
                                                cACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAg             >  1:1168241/1‑69 (MQ=255)
                                                cACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAg             >  1:937965/1‑69 (MQ=255)
                                                cACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAg             >  1:2223626/1‑69 (MQ=255)
                                                cACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAg             >  1:1303391/1‑69 (MQ=255)
                                                   cTTTCGGTTGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:751307/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAATCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2795736/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCTTTGAGtt           <  1:989508/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:547643/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:1232324/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:1183199/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:951267/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:968834/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:127602/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:3204103/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2584113/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:189415/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2081545/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2171567/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:1724151/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2533698/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2571896/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:2623115/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:268035/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:3058814/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:3161953/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:1573597/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:3181436/68‑1 (MQ=255)
                                                   cTTTCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:3375514/68‑1 (MQ=255)
                                                    tttCGGTGGGTCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGtt           <  1:324139/67‑1 (MQ=255)
                                                           ggATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAgg   >  1:3414379/1‑68 (MQ=255)
                                                           ggATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAGGc  >  1:111599/1‑69 (MQ=255)
                                                           ggATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAGGc  >  1:25053/1‑69 (MQ=255)
                                                             |                                                                  
CTACGGACGAGGTGCTGCCCATGGTGTATACACCAGTAATTGGAAGCTCACCTTTCGGCGGATCCTGTACTGACATTCCACGATACAGTTCAAGCTCGTTCAGGTAGTGGCGTTGAGTTTCATCAGGC  >  minE/2407139‑2407266

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