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 1,521,050 A→T 45.5% G284G (GGT→GGA)  usg ← predicted semialdehyde dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,521,0500AT45.5% 17.4 / 97.4 88G284G (GGT→GGA) usgpredicted semialdehyde dehydrogenase
Reads supporting (aligned to +/- strand):  ref base A (37/11);  new base T (23/17);  total (60/28)
Fisher's exact test for biased strand distribution p-value = 6.65e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.01e-01

Only 100 of 107 total aligned reads displayed.

CCGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCACG  >  minE/1520997‑1521118
                                                     |                                                                    
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGACGCATCa                                                                      <  1:440425/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:3324898/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:2318018/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:1183177/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:822343/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:812593/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:2348780/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:2367269/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCa                                                                      <  1:2834605/54‑1 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:3306948/1‑69 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:2968388/1‑69 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:507469/1‑69 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:2964536/1‑69 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:1449471/1‑69 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:812344/1‑69 (MQ=255)
ccGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTggg                                                       >  1:2316729/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:190093/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:2880008/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:231634/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:8543/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:1608720/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:13738/1‑69 (MQ=255)
        aTTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGta                                               >  1:3248429/1‑68 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGtt                                               >  1:2501395/1‑66 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTtc                                              >  1:1840170/1‑67 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTtc                                              >  1:554177/1‑67 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTtc                                              >  1:1068948/1‑67 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTtc                                              >  1:2056321/1‑67 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTtc                                              >  1:645991/1‑67 (MQ=255)
           acgcacgcAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTtc                                              >  1:2127598/1‑67 (MQ=255)
               acgcaGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCa                                        <  1:586602/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:1051645/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:83760/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:673860/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2368990/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2636568/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2937442/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2942372/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2946196/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:3345194/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2279450/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:104477/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:1780092/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:1723841/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:1286154/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:1720444/69‑1 (MQ=255)
                  caGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:1637491/69‑1 (MQ=255)
                   aGCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGTCGGGAATTCGTTCTCTTCagag                                     <  1:2821913/68‑1 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:1792673/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:959225/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:3013989/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:400520/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:624308/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:631463/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:748881/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:1241144/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:83741/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:881412/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:894319/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2222749/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2164771/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2431650/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:1963662/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2431918/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2434335/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2122933/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:276878/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:2000350/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGtc                                                          >  1:287370/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGt                                                           >  1:1893761/1‑45 (MQ=255)
                    gCCAACGGAAAGATGCGGCGTACCAGAAGCATCTCCTACCTGAGt                                                           >  1:914394/1‑45 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCAGAATATCTTCGCCTTGAACa             <  1:303658/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAAc              >  1:581192/1‑68 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             >  1:1951754/1‑69 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:1230570/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             >  1:754695/1‑69 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             >  1:3074098/1‑69 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             >  1:1355159/1‑69 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:3091120/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:2067073/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             >  1:2637590/1‑69 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:1691770/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:852804/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:3140914/69‑1 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             >  1:2209096/1‑69 (MQ=255)
                                          cccGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:3276610/69‑1 (MQ=255)
                                           ccGAAGCATCACCTACCTGAGTTGTGAATTCGTTCTCTTCATAGAGCACAATATCTTCGCCTTGTACa             <  1:3179286/68‑1 (MQ=255)
                                             gAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACa             <  1:1385137/66‑1 (MQ=255)
                                                gCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGc        >  1:1217813/1‑68 (MQ=255)
                                                gCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGc        >  1:1909687/1‑68 (MQ=255)
                                                gCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGc        >  1:1741395/1‑68 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:758340/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:1668424/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:1860415/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:1081183/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:274060/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:2178146/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:2188613/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:333893/1‑69 (MQ=255)
                                                     acctacctGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCAcg  >  1:2954312/1‑69 (MQ=255)
                                                     |                                                                    
CCGTAGTCATTACGCACGCAGCCAACAGAAAGATGCGGCGTACCCGAAGCATCACCTACCTGAGTTGGGAATTCGTTCTCTTCAGAGAGCACAATATCTTCGCCTTGAACAAACGCATCACG  >  minE/1520997‑1521118

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