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 260,895 G→T 59.2% A142A (GCC→GCA)  yajI ← predicted lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE260,8950GT59.2% 23.7 / 75.3 76A142A (GCC→GCA) yajIpredicted lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (25/6);  new base T (29/16);  total (54/22)
Fisher's exact test for biased strand distribution p-value = 1.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

CCCTTTAACTGTAACGGAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCATA  >  minE/260842‑260963
                                                     |                                                                    
cccTTTAACTGTAACGGAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGa                                                       <  1:591894/69‑1 (MQ=255)
cccTTTAACTGTAACGGAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGa                                                       <  1:2590164/69‑1 (MQ=255)
cccTTTAACTGTAACGGAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGa                                                       <  1:2622801/69‑1 (MQ=255)
                gAATATCAACATCGCTGGGGGCGAGGCCGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGAttt                                       >  1:371002/1‑69 (MQ=255)
                gAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGAttt                                       >  1:962114/1‑69 (MQ=255)
                gAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGAttt                                       >  1:859371/1‑69 (MQ=255)
                gAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGAttt                                       >  1:2365008/1‑69 (MQ=255)
                gAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGAttt                                       >  1:1322804/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGAttt                                       >  1:1567018/1‑68 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGAttt                                       >  1:1692284/1‑68 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGAttt                                       >  1:1890405/1‑68 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:2949662/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:204306/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:1461499/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:2629295/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:2762649/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:2787282/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:1334290/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:3236326/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:1258486/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:595308/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:950764/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTc                                      >  1:998914/1‑69 (MQ=255)
                 aaTATCAACATCGCTGGGGGCGAGGACGCTGGCAGGTGCCTTAATCAAATGATTCTGCACATTGATTTc                                      >  1:2291087/1‑69 (MQ=255)
                  atatCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTc                                      >  1:1185123/1‑68 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTcc                                     >  1:60785/1‑66 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:2241316/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:2232063/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:2252031/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:1502996/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:368027/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:1250224/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:1190264/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:2430326/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:2433610/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:1804795/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:1776068/1‑67 (MQ=255)
                     tCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCt                                    >  1:1036301/1‑67 (MQ=255)
                       aaCATCGCTGGGGGCGATGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGaaa                                >  1:977332/1‑69 (MQ=255)
                       aaCATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGaaa                                >  1:2443085/1‑69 (MQ=255)
                       aaCATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGaaa                                >  1:2556011/1‑69 (MQ=255)
                       aaCATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGaaa                                >  1:1722261/1‑69 (MQ=255)
                             gCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTc                          >  1:2826712/1‑69 (MQ=255)
                             gCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTc                          >  1:339572/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:3131902/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:2804590/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1601506/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1129256/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:10869/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1426084/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:2701517/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1651891/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1543256/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1566130/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:150332/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:1003662/1‑69 (MQ=255)
                                 ggggCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTAtt                      >  1:2290791/1‑69 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:644580/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1938499/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:773224/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1968276/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1478829/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:805717/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1311261/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1864115/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:3197452/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:90376/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1102282/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1418750/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1419209/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:2758874/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:97566/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGTGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:252709/69‑1 (MQ=255)
                                    gCGAGGACGCTGGCAGGGGCGTTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGtt                   <  1:1859520/69‑1 (MQ=255)
                                         gACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTg              <  1:1395049/69‑1 (MQ=255)
                                          aCGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTg              <  1:2141304/68‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:3377986/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:745672/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:1952920/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  >  1:3264272/1‑69 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:322949/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:2197941/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  >  1:2839884/1‑69 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  >  1:2766644/1‑69 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:2301261/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  <  1:2645869/69‑1 (MQ=255)
                                                     ggCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCata  >  1:1470136/1‑69 (MQ=255)
                                                     |                                                                    
CCCTTTAACTGTAACGGAATATCAACATCGCTGGGGGCGAGGACGCTGGCAGGGGCATTAATCAATTGATTCTGCACATTGATTTCCTGAAAGTTGTCTATTGTTCCCTGAATTTGCCCATA  >  minE/260842‑260963

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