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 2,212,202 G→C 41.2% L292L (CTC→CTG)  rng ← ribonuclease G

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,212,2020GC41.2% 42.8 / 84.2 85L292L (CTC→CTG) rngribonuclease G
Reads supporting (aligned to +/- strand):  ref base G (28/22);  new base C (11/24);  total (39/46)
Fisher's exact test for biased strand distribution p-value = 2.92e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

ACCGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGAC  >  minE/2212142‑2212264
                                                            |                                                              
aCCGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAacc                                                        <  1:2262353/69‑1 (MQ=255)
aCCGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAacc                                                        <  1:725737/69‑1 (MQ=255)
aCCGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAacc                                                        <  1:658176/69‑1 (MQ=255)
aCCGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAacc                                                        <  1:3150058/69‑1 (MQ=255)
 ccGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAacc                                                        <  1:2560138/68‑1 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:1866371/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:2696959/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:3043238/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:2305126/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:2204141/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:2130325/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:1868911/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:3324049/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:3385851/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:747080/1‑68 (MQ=255)
              cGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATCAGATAACCACCGGATTTCAGt                                           >  1:1297738/1‑68 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:973772/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:337632/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:2794699/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:280039/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:3028861/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:2281850/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:1390023/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:3135805/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:591143/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:2022505/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:3180517/44‑1 (MQ=255)
                     gATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGAt                                                            <  1:1851452/44‑1 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:367411/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:823808/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:351106/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:2801501/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:903468/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:2016286/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:2145394/1‑69 (MQ=255)
                        gTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:1618263/1‑69 (MQ=255)
                        gTCCACGGTGGACATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCg                                >  1:516507/1‑69 (MQ=255)
                                tggtCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2870694/69‑1 (MQ=255)
                                tggtCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:1339439/69‑1 (MQ=255)
                                tggtCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:256616/69‑1 (MQ=255)
                                tggtCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:3432416/69‑1 (MQ=255)
                                    cATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGGGTTCCAGcgctcg                    >  1:697575/1‑69 (MQ=255)
                                    cATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGcgctcg                    >  1:2796637/1‑69 (MQ=255)
                                    cATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGcgctcg                    >  1:1220397/1‑69 (MQ=255)
                                    cATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGcgctcg                    >  1:696648/1‑69 (MQ=255)
                                        gCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTgg                >  1:805942/1‑69 (MQ=255)
                                        gCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTgg                >  1:1269784/1‑69 (MQ=255)
                                        gCTTCGGTCTGGTCGATAATGAGATAACCACC‑GATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTg                 >  1:3425728/1‑67 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCGgcg                        <  1:509514/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:34746/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:587988/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:349679/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:1548614/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:1543402/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:377464/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:552203/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:1126978/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:795768/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:122397/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:922563/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2585808/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:1579889/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:3230057/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:318448/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2700382/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2774236/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:3103242/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:3081093/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2336658/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:1023879/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2967550/53‑1 (MQ=255)
                                                cTGGTCGATAATCAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2362659/53‑1 (MQ=255)
                                                   gTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGtttt      >  1:691009/1‑68 (MQ=255)
                                                   gTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTc     >  1:1744289/1‑69 (MQ=255)
                                                   gTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTc     >  1:1362975/1‑69 (MQ=255)
                                                   gTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTc     >  1:1469150/1‑69 (MQ=255)
                                                   gTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTc     >  1:3037346/1‑69 (MQ=255)
                                                   gTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTc     >  1:374280/1‑69 (MQ=255)
                                                      gATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGa   >  1:2908600/1‑68 (MQ=255)
                                                      gATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGa   >  1:2156458/1‑68 (MQ=255)
                                                      gATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGa   >  1:2713705/1‑68 (MQ=255)
                                                      gATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGAc  >  1:2471394/1‑69 (MQ=255)
                                                      gATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGAc  >  1:900004/1‑69 (MQ=255)
                                                      gATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGAc  >  1:2693470/1‑69 (MQ=255)
                                                           tGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAgcg                        <  1:2417432/42‑1 (MQ=255)
                                                            |                                                              
ACCGACAAACGCTCCGGTATTGATGTCCACGGTGGTCATCGCTTCGGTCTGGTCGATAATGAGATAACCACCGGATTTCAGTTCTACTTTGCGTTCCAGCGCTCGCTGGATTTCGTTTTCGAC  >  minE/2212142‑2212264

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