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 1,687,119 C→T 54.0% P167P (CCG→CCA)  sseB ← rhodanase‑like enzyme, sulfur transfer from thiosulfate

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,687,1190CT54.0% 7.2 / 63.2 76P167P (CCG→CCA) sseBrhodanase‑like enzyme, sulfur transfer from thiosulfate
Reads supporting (aligned to +/- strand):  ref base C (10/25);  new base T (25/16);  total (35/41)
Fisher's exact test for biased strand distribution p-value = 5.96e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAATAAGTAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCG  >  minE/1687054‑1687179
                                                                 |                                                            
ccAATAAGTAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCgg                                                            >  1:830394/1‑68 (MQ=255)
ccAATAAGTAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCgg                                                            >  1:2830397/1‑68 (MQ=255)
ccAATAAGTAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCgg                                                            >  1:3146249/1‑68 (MQ=255)
        tAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATgg                                                    <  1:1030440/68‑1 (MQ=255)
        tAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATgg                                                    <  1:2141816/68‑1 (MQ=255)
        tAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATgg                                                    <  1:307934/68‑1 (MQ=255)
        tAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATgg                                                    <  1:400199/68‑1 (MQ=255)
         aaaTTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATgg                                                    <  1:1522614/67‑1 (MQ=255)
                gCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAAt                                            <  1:2164210/68‑1 (MQ=255)
                gCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAAt                                            <  1:661289/68‑1 (MQ=255)
                      ccTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAggtg                                      >  1:762609/1‑68 (MQ=255)
                      ccTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAggtg                                      >  1:2978985/1‑68 (MQ=255)
                      ccTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAggtg                                      >  1:1151105/1‑68 (MQ=255)
                      ccTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAggt                                       <  1:2982598/67‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:498359/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:2562051/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:1079694/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:2958389/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:3238436/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:1571111/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:3243675/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:3284930/69‑1 (MQ=255)
                        tctTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   <  1:1509170/69‑1 (MQ=255)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTTGCTTAATGGt                                                   >  1:2327922/1‑52 (MQ=37)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTTATGGtt                                                  >  1:401431/1‑53 (MQ=37)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:855242/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:3435121/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:356982/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:364442/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:656591/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:2646152/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:45460/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:2599791/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:638336/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:252414/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:1547706/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:1024710/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:2389343/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:1766937/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:1176590/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:2098999/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:1233346/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:2012175/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:2005167/1‑53 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGt                                                   >  1:2308446/1‑52 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGt                                                   >  1:630532/1‑52 (MQ=38)
                         ctTCGCTCTCTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGt                                                   >  1:618942/1‑52 (MQ=38)
                         ctTCGCTCACTTTAATTAAACAAATAAAAGCACGCTTCACTGGCTTAATGGtt                                                  >  1:1369907/1‑53 (MQ=37)
                          ttCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGgtggtg                                   >  1:2969928/1‑67 (MQ=255)
                                     tAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAatcaatca                      >  1:1533930/1‑69 (MQ=255)
                                     tAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAatcaatca                      >  1:1255228/1‑69 (MQ=255)
                                     tAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAatcaatca                      >  1:2632376/1‑69 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGTCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1115742/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1275153/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:127641/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:37344/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1003483/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1764271/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:3080911/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:2533088/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:2315326/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:2145851/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1882833/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:3055564/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1866774/63‑1 (MQ=255)
                                            aCAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1370260/63‑1 (MQ=255)
                                             cAAATAAAAGCACGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:1245560/62‑1 (MQ=255)
                                                        aCGCTTCACTGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCAt                     <  1:2968036/51‑1 (MQ=255)
                                                        aCGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGc   <  1:580047/69‑1 (MQ=255)
                                                         cGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:1259598/69‑1 (MQ=255)
                                                         cGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:2978127/69‑1 (MQ=255)
                                                         cGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:285449/69‑1 (MQ=255)
                                                         cGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:2841343/69‑1 (MQ=255)
                                                         cGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:700437/69‑1 (MQ=255)
                                                         cGCTTCACCGCCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:2550302/69‑1 (MQ=255)
                                                          gCTTCACCGGCTTAATGGTTTTAAATAAGGTTGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCg  <  1:1337590/68‑1 (MQ=255)
                                                                 |                                                            
CCAATAAGTAAATTAGGCTGTGCCTCTTCGTTCTCTTTAATTGAACAAATAAAAGCACGCTTCACCGGCTTAATGGTTTTAAATAAGGTGGTGAGTGAATCAATCATTTGTGCTGGCGGCTCTGCG  >  minE/1687054‑1687179

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