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 2,904,485 C→T 45.4% A537T (GCC→ACC)  treC ← trehalose‑6‑P hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,904,4850CT45.4% 10.9 / 51.7 66A537T (GCC→ACC) treCtrehalose‑6‑P hydrolase
Reads supporting (aligned to +/- strand):  ref base C (15/21);  new base T (9/21);  total (24/42)
Fisher's exact test for biased strand distribution p-value = 4.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.03e-01

ACCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGCCCT  >  minE/2904419‑2904552
                                                                  |                                                                   
aacGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCAGTAAATTCATGGcac                                                                   >  1:461933/3‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:101764/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:2562055/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:2899975/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:2920128/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:2177944/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:3219283/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:3355044/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:351514/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:174519/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:170473/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:578141/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:160288/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:1052824/1‑69 (MQ=255)
aCCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGcac                                                                   >  1:1214889/1‑69 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:776951/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:2752034/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:254015/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:276873/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:279697/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:976489/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:2324164/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:938414/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:296149/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:3118947/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:1191151/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:3282110/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:1244261/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:382286/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:834121/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:779237/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:1469196/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:168339/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:498137/66‑1 (MQ=255)
            cgAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:16698/66‑1 (MQ=255)
              aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                                     >  1:932581/1‑69 (MQ=255)
              aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                                     >  1:3051740/1‑69 (MQ=255)
              aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                                     >  1:2694572/1‑69 (MQ=255)
              aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                                     >  1:2602666/1‑69 (MQ=255)
              aaGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAg                                                     >  1:1121701/1‑69 (MQ=255)
                gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                                   <  1:2663494/69‑1 (MQ=255)
                gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                                   <  1:1202209/69‑1 (MQ=255)
                gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                                   <  1:652555/69‑1 (MQ=255)
                gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                                   <  1:519656/69‑1 (MQ=255)
                gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                                   <  1:1896624/69‑1 (MQ=255)
                gATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGc                                                   <  1:3320356/69‑1 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:2692770/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:1528834/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:1673197/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:3370858/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:1949194/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:2144786/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:3195811/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGcttc                                                >  1:2321545/1‑69 (MQ=255)
                   ttACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTGTGGTGAGGctt                                                 >  1:1758455/1‑68 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                                        <  1:3335019/66‑1 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                                        <  1:1370039/66‑1 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                                        <  1:2461464/66‑1 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                                        <  1:1661010/66‑1 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGt                                        <  1:687468/66‑1 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTa                                      >  1:1972808/1‑68 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTa                                      >  1:2987456/1‑68 (MQ=255)
                              accaccAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTa                                      >  1:2371386/1‑68 (MQ=255)
                                caccaGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGc                                   >  1:1250643/1‑69 (MQ=255)
                                    aGACAGCCTCAAAAGGCCGTAAAGTCATGGTACAGGGTTgtgg                                                         <  1:2882229/43‑1 (MQ=255)
                                                       tAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCcgcg            <  1:2251286/69‑1 (MQ=255)
                                                       tAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCcgcg            <  1:2318028/69‑1 (MQ=255)
                                                         aaTTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCgcgc           >  1:2316415/1‑68 (MQ=255)
                                                         aaTTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCgcgc           >  1:1163344/1‑68 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTgg     <  1:273769/68‑2 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:62935/68‑1 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:2385157/68‑1 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:579682/68‑1 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:1874995/68‑1 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:377206/68‑1 (MQ=255)
                                                               tGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:2913406/68‑1 (MQ=255)
                                                               tGGCAAAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGc     <  1:774820/68‑1 (MQ=255)
                                                                 gCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGCcct  >  1:742989/1‑69 (MQ=255)
                                                                 gCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGCcct  >  1:369419/1‑69 (MQ=255)
                                                                 gCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGCcct  >  1:2544192/1‑69 (MQ=255)
                                                                 gCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGCcct  >  1:997946/1‑69 (MQ=255)
                                                                  |                                                                   
ACCGGGGCTTAGGGAAGATTTACTTCTGTAACCACCAGACAGCCTCAAAAGGCCGTAAATTCATGGCACAGGGTTGTGGTGAGGCTTCTTCGTAGTTATGCATCACAAGCTGCCAGTTGCCGCGCATTTGCCCT  >  minE/2904419‑2904552

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