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 260,678 G→A 37.9% intergenic (‑196/+103) tsx ← / ← yajI nucleoside channel, receptor of phage T6 and colicin K/predicted lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE260,6780GA37.9% 45.7 / 48.3 79intergenic (‑196/+103)tsx/yajInucleoside channel, receptor of phage T6 and colicin K/predicted lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (8/41);  new base A (14/16);  total (22/57)
Fisher's exact test for biased strand distribution p-value = 4.82e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTATCATTTACGTAATCGATTGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAT  >  minE/260612‑260733
                                                                  |                                                       
cTATCATTTACGTAATCGATTGCGTTCACGTTTACACACATTTGGGCGGGGATTGTACTGACTTTCGcc                                                       >  1:800152/1‑69 (MQ=255)
cTATCATTTACGTAATCGATTGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGcc                                                       >  1:407254/1‑69 (MQ=255)
cTATCATTTACGTAATCGATTGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGc                                                        >  1:1026440/1‑68 (MQ=255)
       ttACGTAATCGATTGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttgtt                                                 >  1:1173013/1‑68 (MQ=255)
       ttACGTAATCGATTGCGTTCACGTTTACAAACATTCGGGCGGGGATTGTACTGACTTTCGCCCttgtt                                                 >  1:403711/1‑68 (MQ=255)
          cGTAATCGATTGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCa                                              <  1:1593630/68‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTAc                                     <  1:1452563/68‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTAc                                     <  1:3295838/68‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTAc                                     <  1:716370/68‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTAc                                     <  1:858188/68‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:131630/69‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:2823563/69‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:1026582/69‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:1009036/69‑1 (MQ=255)
                   ttGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:1305555/69‑1 (MQ=255)
                   ttGAGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:623844/69‑1 (MQ=255)
                       gTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATc                                 <  1:1280146/68‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:1480890/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:176245/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:369245/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:3417130/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:66492/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:3032334/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:2369602/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCttg                                                   <  1:2348108/47‑1 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTGTCaa                               >  1:1409814/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:474758/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:913348/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:2763718/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:2690705/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:2133714/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:2118489/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:145814/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:135861/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCaa                               >  1:1450157/1‑67 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCa                                >  1:1306158/1‑66 (MQ=255)
                          cACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCATTGTTGCAAACTTTTACTATCaa                               >  1:795228/1‑67 (MQ=255)
                          cACGTTTACACACATT‑GGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            >  1:1118165/1‑69 (MQ=255)
                          cACGTTTAAACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCa                                >  1:3146316/1‑66 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcg                            <  1:2976991/68‑2 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:529464/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:545837/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:727588/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:3433476/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:1933583/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:739466/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:796980/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:3058616/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:2192319/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:2360191/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:2532893/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:1979669/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:2885347/68‑1 (MQ=255)
                            cGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:2746567/68‑1 (MQ=255)
                             gTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAg                          <  1:372095/69‑1 (MQ=255)
                             gTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAg                          <  1:2172748/69‑1 (MQ=255)
                             gTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAg                          <  1:1958318/69‑1 (MQ=255)
                             gTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAg                          <  1:1965088/69‑1 (MQ=255)
                             gTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAg                          <  1:1970036/69‑1 (MQ=255)
                             gTTTACACACATTCGGGCGGGGATTGTACTGACTTTCACCCTTGTTGCAAACTTTTACTATCAATcc                            <  1:3426280/67‑1 (MQ=255)
                                   acacaTTCGGG‑GGGGATTGTACTGACTTTCGCCCTTGTTGCAAACt                                          <  1:2752240/46‑1 (MQ=39)
                                    cacaTTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGt                   <  1:2212373/69‑1 (MQ=255)
                                    cacaTTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGt                   <  1:1348331/69‑1 (MQ=255)
                                    cacaTTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGt                   <  1:1492094/69‑1 (MQ=255)
                                    cacaTTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGt                   <  1:1868521/69‑1 (MQ=255)
                                    cacaTTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGt                   <  1:1917019/69‑1 (MQ=255)
                                         tCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCa              <  1:1228207/69‑1 (MQ=255)
                                          cgggcgggGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    >  1:2025634/1‑46 (MQ=255)
                                          cgggcgggGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCag             >  1:265684/1‑69 (MQ=255)
                                          cgggcgggGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCag             >  1:2706629/1‑69 (MQ=255)
                                                   aTTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:2624361/37‑1 (MQ=255)
                                                    ttGTACTGACTTTCGCCCTTGTTGCAAACTTTTAc                                     <  1:3048299/35‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACt                                    <  1:1143460/35‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAt  <  1:2952932/69‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAt  <  1:2994174/69‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAt  <  1:2557524/69‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAt  <  1:2676341/69‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAt  <  1:352411/69‑1 (MQ=255)
                                                     tGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAt  <  1:3084174/69‑1 (MQ=255)
                                                                  |                                                       
CTATCATTTACGTAATCGATTGCGTTCACGTTTACACACATTCGGGCGGGGATTGTACTGACTTTCGCCCTTGTTGCAAACTTTTACTATCAATCCAGGTGATGTAAGCAGAGTAACAAAAT  >  minE/260612‑260733

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