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 1,361,205 T→A 50.5% intergenic (‑198/+65) yehE ← / ← mrp hypothetical protein/antiporter inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,361,2050TA50.5% 5.3 / 146.6 121intergenic (‑198/+65)yehE/mrphypothetical protein/antiporter inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (11/49);  new base A (10/51);  total (21/100)
Fisher's exact test for biased strand distribution p-value = 8.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 126 total aligned reads displayed.

GAGTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGTTAATAGGCGTTAG  >  minE/1361138‑1361273
                                                                   |                                                                    
gagTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACt                                                                      <  1:1754273/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGTCAAAAACTaa                                                                    <  1:3299188/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:2479916/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:1828694/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:1538186/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:2572574/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:2195915/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:1868170/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:818827/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:1367196/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:3245553/68‑1 (MQ=255)
  gTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    <  1:1462208/68‑1 (MQ=255)
                tCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGc                                                            <  1:95464/62‑1 (MQ=255)
                tCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGc                                                            <  1:3160421/62‑1 (MQ=255)
                tCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGc                                                            <  1:1240059/62‑1 (MQ=255)
                tCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGc                                                            <  1:870831/62‑1 (MQ=255)
                 ccGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGt                                                    >  1:876673/1‑69 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1954960/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:2904039/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:281574/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1837117/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:3255228/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1621093/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1084957/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1258470/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:84475/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:718615/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:376908/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:447699/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1559101/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:57965/69‑1 (MQ=255)
                        atatTCGCAGCATTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACAtct                                             <  1:1484219/69‑1 (MQ=255)
                         tatTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATc                                                         >  1:1649863/1‑56 (MQ=255)
                         tatTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACAtctc                                            >  1:1852856/1‑69 (MQ=255)
                         tatTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACAtctc                                            >  1:3389299/1‑69 (MQ=255)
                           ttCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTaa                                                                    >  1:714473/1‑43 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:449861/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:2040051/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:168495/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:2722616/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:3272652/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:1256015/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:2425795/1‑69 (MQ=255)
                              gcagcaTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGCg                                        >  1:107406/1‑68 (MQ=255)
                                   aTTAAATAAGTGTTCATTAATGCGGCAAAAACAAATACACCGCATCTATGTAACAtct                                             <  1:931049/58‑1 (MQ=255)
                                    ttAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTa                                   >  1:1597462/1‑67 (MQ=255)
                                         tAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCgg                                       >  1:375344/1‑58 (MQ=255)
                                         tAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATgaaga                             >  1:1145508/1‑68 (MQ=255)
                                             tgtTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAAc                        <  1:2261479/69‑1 (MQ=255)
                                             tgtTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAAc                        <  1:3077033/69‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:2159584/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:2028140/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:54885/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:296737/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:2050905/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:594506/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:2703541/68‑1 (MQ=255)
                                                 cATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAg                     <  1:935912/68‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:1870833/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:3327026/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:1269574/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:1201648/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:2976793/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:2234728/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATgg                <  1:2366854/69‑1 (MQ=255)
                                                     aaTGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATg                 >  1:1034249/1‑68 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:1580738/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:3436437/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:359548/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2422338/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:1532765/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:485324/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:1444585/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:683467/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:1378690/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:849111/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2597768/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:3351284/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2650341/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2656601/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:270829/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2732323/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2054002/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:3222991/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2981412/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAACAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2899092/44‑1 (MQ=255)
                                                     aaTGCGGCAAAAAAAAATACACCGCATCAATGTAACATCTCTGc                                         <  1:2341433/44‑1 (MQ=38)
                                                       tGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGt               <  1:3308082/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:2865017/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:1440337/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:804715/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:1294681/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:1626134/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:2648596/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:1612804/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:2526768/68‑1 (MQ=255)
                                                        gCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:3391193/68‑1 (MQ=255)
                                                         cGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGtt              <  1:1731890/67‑1 (MQ=255)
                                                                   tAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGTTAATAGGCGTTAg  <  1:467874/69‑1 (MQ=255)
                                                                   tAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGTTAATAGGCGTTAg  <  1:1676166/69‑1 (MQ=255)
                                                                   |                                                                    
GAGTTTCGGACGAAGGTCCGCAGAATATTCGCAGTATTAAATAAGTGTTCATTAATGCGGCAAAAACTAATACACCGCATCAATGTAACATCTCTGCGGTGTATGAAGAATAACCAGAATGGTTAATAGGCGTTAG  >  minE/1361138‑1361273

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A