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 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 558,918 T→C 28.0% P55P (CCT→CCC)  cmr → multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE558,9180TC28.0% 33.1 / 16.0 25P55P (CCT→CCC) cmrmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (7/11);  new base C (4/3);  total (11/14)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

ATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCT  >  minE/558854‑558977
                                                                |                                                           
atatGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTc                                                        <  1:116687/70‑1 (MQ=255)
atatGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTc                                                        <  1:134929/70‑1 (MQ=255)
 tatGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCg                                                       <  1:576695/70‑1 (MQ=255)
   tGATTCAACCCGGTATGTTGTCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATg                                                    <  1:57165/71‑1 (MQ=255)
     aTTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGAc                                                  >  1:2066880/1‑71 (MQ=255)
               gTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTg                                        >  1:349483/1‑71 (MQ=255)
                       gCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGgcgggcgg                                >  1:1216877/1‑71 (MQ=255)
                                 aaCAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGa                                                   >  1:1941440/1‑42 (MQ=255)
                                 aaCAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTa                      <  1:674788/71‑1 (MQ=255)
                                  aCAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTa                      >  1:1545093/1‑70 (MQ=255)
                                    aaTATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa                   <  1:1706724/71‑1 (MQ=255)
                                       atCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc                     <  1:305816/66‑1 (MQ=255)
                                          aGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCTGGATGTTTTTAc                     <  1:381699/63‑1 (MQ=255)
                                            gCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACaa                   >  1:380302/1‑63 (MQ=255)
                                                 cATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGttttt                       <  1:495198/54‑1 (MQ=255)
                                                   ttgattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGttttt                       <  1:901820/52‑1 (MQ=255)
                                                   ttgattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGtttt                        <  1:1361961/51‑1 (MQ=255)
                                                     gattgGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCt  >  1:707504/1‑71 (MQ=255)
                                                     gattgGGTTCCCACTTCGATGACCGCGTATCTggcg                                     >  1:170009/1‑36 (MQ=255)
                                                     gattgGGTTCCCACTTCGATGACCGCGTATCTggcg                                     >  1:396799/1‑36 (MQ=255)
                                                     gattgGGTTCCCACTTCGATGACCGCGTATCTggcg                                     >  1:1770620/1‑36 (MQ=255)
                                                           gTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGgc               <  1:1442965/52‑1 (MQ=255)
                                                           gTTCCCACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATg                 <  1:1403668/50‑1 (MQ=255)
                                                            ttCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc                     <  1:2080588/45‑1 (MQ=255)
                                                              ccTACTTCGATGACCGCGTATCTGGCGAGCGGGATGTTTTTACaa                   >  1:202320/1‑45 (MQ=255)
                                                                tACTTCGATGACCGCGTATCTGGCGGGCGGGATGtttt                        >  1:2049659/1‑38 (MQ=255)
                                                                tACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTAc                     <  1:934381/41‑1 (MQ=255)
                                                                |                                                           
ATATGATTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAATGGCTGCTGGGGCCGCT  >  minE/558854‑558977

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