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 424,830 C→T 32.4% A22A (GCG→GCA)  nagC ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE424,8300CT32.4% 68.7 / 38.7 80A22A (GCG→GCA) nagCDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base C (18/36);  new base T (17/9);  total (35/45)
Fisher's exact test for biased strand distribution p-value = 8.69e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGCTTTGCTCGGCAATCTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGGT  >  minE/424767‑424890
                                                               |                                                            
cTGGCTTTGCTCGGCAATCTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACcgccgc                                                         >  1:2926748/1‑69 (MQ=255)
                  cTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGtttt                                         >  1:279063/1‑67 (MQ=255)
                  cTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGtttt                                         >  1:3295128/1‑67 (MQ=255)
                  cTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGtttt                                         >  1:260305/1‑67 (MQ=255)
                  cTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGtttt                                         >  1:20816/1‑67 (MQ=255)
                   tGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGt                                            >  1:2206643/1‑63 (MQ=255)
                   tGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGt                                            >  1:3296627/1‑63 (MQ=255)
                   tGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGt                                            >  1:3429040/1‑63 (MQ=255)
                   tGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGt                                            >  1:676566/1‑63 (MQ=255)
                       tCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACgag                                    <  1:590665/67‑1 (MQ=255)
                       tCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACgag                                    <  1:2556339/67‑1 (MQ=255)
                       tCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACgag                                    <  1:2878428/67‑1 (MQ=255)
                           cgAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAAc                              <  1:480979/69‑1 (MQ=255)
                           cgAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAAc                              <  1:2614387/69‑1 (MQ=255)
                           cgAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAAc                              <  1:3301784/69‑1 (MQ=255)
                           cgAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAAc                              <  1:2069733/69‑1 (MQ=255)
                           cgAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAAc                              <  1:1219114/69‑1 (MQ=255)
                               aTTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAAc                              <  1:1170969/65‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTg                  <  1:228671/69‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTg                  <  1:3364670/69‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTg                  <  1:1516375/69‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTg                  <  1:1359001/69‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTg                  <  1:66533/69‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACATATCTg                  <  1:1839602/69‑1 (MQ=255)
                                       gTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTAAGAGATCAACATTACCTATCTg                  <  1:329807/69‑1 (MQ=255)
                                             gTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            >  1:285235/1‑69 (MQ=255)
                                             gTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            >  1:2178192/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            >  1:2914407/1‑68 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            >  1:87277/1‑68 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            >  1:2221477/1‑68 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:2431202/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:2491485/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:2435107/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:2765254/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:297072/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:2921654/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:1173070/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:1219157/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:1723251/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:1364556/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:2025623/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:1673475/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:204214/1‑69 (MQ=255)
                                              tCAATCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGt           >  1:1685897/1‑69 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:1063089/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:2964254/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:3054644/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:3087291/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:3281387/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:1571241/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:1494479/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:1379257/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:664878/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:682691/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:944584/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:2194731/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:1980051/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:874483/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:2094303/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:2608534/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:26758/67‑1 (MQ=255)
                                               cAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTc          >  1:1887513/1‑69 (MQ=255)
                                                aaTCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:2262973/66‑1 (MQ=255)
                                                aaTCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTg            <  1:2648681/66‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:2119319/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:154252/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:3410324/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:68752/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:191788/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:2195691/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:1914000/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGc       <  1:2510398/69‑1 (MQ=255)
                                                  tCAGGCGATAAACTGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATAACCTATCTGAGCTTGTCCGc       <  1:1681080/69‑1 (MQ=255)
                                                      gCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTg    <  1:1648638/68‑1 (MQ=255)
                                                       cGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:972958/1‑69 (MQ=255)
                                                       cGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:3245602/1‑69 (MQ=255)
                                                       cGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:2288046/1‑69 (MQ=255)
                                                        gATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:3252413/1‑68 (MQ=255)
                                                        gATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:2845929/1‑68 (MQ=255)
                                                        gATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:887040/1‑68 (MQ=255)
                                                        gATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGgt  >  1:2540840/1‑68 (MQ=255)
                                                               |                                                            
CTGGCTTTGCTCGGCAATCTGAATCCGCGAGATTGGCCCGTACTGGTCAATCAGGCGATAAACCGCCGCGCTGTTAAGCTGTTTTACGAGATCAACATTACCTATCTGAGCTTGTCCGCCTGGT  >  minE/424767‑424890

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