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 429,921 A→G 36.3% K176K (AAA→AAG)  glnS → glutamyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE429,9210AG36.3% 44.8 / 46.4 77K176K (AAA→AAG) glnSglutamyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base A (28/21);  new base G (26/2);  total (54/23)
Fisher's exact test for biased strand distribution p-value = 7.87e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01

TGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTG  >  minE/429863‑429985
                                                          |                                                                
tGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATgg                                                        >  1:3095346/1‑69 (MQ=255)
tGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATgg                                                        >  1:184310/1‑69 (MQ=255)
tGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATgg                                                        >  1:1450255/1‑69 (MQ=255)
tGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATgg                                                        >  1:653943/1‑69 (MQ=255)
tGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATgg                                                        >  1:148253/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2544054/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2994747/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2961367/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:294460/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2783343/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2775794/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2701220/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:258885/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:3108354/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2261406/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2266410/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2299093/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2518431/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:2403011/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:1734548/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:33587/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:1623218/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:3397771/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:1562050/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:3405021/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:389397/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:773522/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:795863/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:866878/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCg                                                >  1:1087211/1‑69 (MQ=255)
        aaaaTGCGTACCGGCGGTTTAGAAGAAGGTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTc                                                    >  1:25171/1‑65 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:1109641/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:3143217/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:2612619/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:702240/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:1565534/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:2438195/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:1786528/1‑69 (MQ=255)
            tGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTa                                            >  1:1981752/1‑69 (MQ=255)
                tGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGt                                        <  1:1959853/69‑1 (MQ=255)
                       ggtTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGa                                                             >  1:2713001/1‑41 (MQ=255)
                       ggtTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATgcgc                                 >  1:642476/1‑69 (MQ=255)
                                   ggTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCGTTTATCGTGATGCGCGATCCGGTGCTg                     <  1:3114090/69‑1 (MQ=255)
                                   ggTAAAGCCTGCCTGCGTGCGAAGATCGACATGGCTTCGCCGTTTATCGTGATGCGCGATCCGGTGCTg                     <  1:768106/69‑1 (MQ=255)
                                     tAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTa                   >  1:2369693/1‑69 (MQ=255)
                                     tAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTa                   >  1:165257/1‑69 (MQ=255)
                                     tAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTa                   >  1:383954/1‑69 (MQ=255)
                                     tAAAGCATGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTa                   >  1:52923/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:2389804/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:1528355/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:760422/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:1431230/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:2053594/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:872574/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:2259646/41‑1 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:1480220/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:1248436/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:386252/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:946653/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:380953/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:2206456/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:2732282/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:2792997/1‑69 (MQ=255)
                                      aaaGCCTGCCTGCGTGCGAAAAGCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTAc                  >  1:3142454/1‑69 (MQ=255)
                                       aaGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGtt                                              <  1:579818/40‑1 (MQ=255)
                                                    tgcgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTg     <  1:1763067/68‑1 (MQ=255)
                                                    tgcgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTg     <  1:195312/68‑1 (MQ=255)
                                                    tgcgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTg     <  1:1467800/68‑1 (MQ=255)
                                                    tgcgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGAGATCCGGTGCTGTACCGTATTAAATTTg     <  1:2134135/68‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:1883385/69‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:1870957/69‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:3093585/69‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:1825980/69‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:1332111/69‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:261337/69‑1 (MQ=255)
                                                      cgAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:1553901/69‑1 (MQ=255)
                                                       gAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTg  <  1:634950/68‑1 (MQ=255)
                                                          |                                                                
TGTTCGAAAAAATGCGTGCCGGTGGTTTTGAAGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTG  >  minE/429863‑429985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A