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
A3 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,326,034 A→G intergenic (‑293/+365) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,326,0340AG94.4% 37.8 / ‑4.1 18intergenic (‑293/+365)yjdN/yjdMmetalloprotein superfamily protein/zinc‑ribbon family protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (6/11);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 3.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

CCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTCGGCACCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTTGGCA  >  NC_000913/4325907‑4326145
                                                                                                                               |                                                                                                               
ccTGATAAGACGCGCAAGCGTCGCATCAGGCAGTCGGCACCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCa                                                                                                      <  1:306688/139‑1 (MQ=255)
             gcAAGCGTCGCATCAGGCAGTCGGCACCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATg                                                                                         <  2:151921/139‑1 (MQ=37)
              cAAGCGTCGCATCAGGCAGTCGGCACCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTCGGCACCGTTGCCGGATgc                                                                                        >  2:1043979/1‑139 (MQ=39)
                              cAGTCGGCACCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCCTCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAACCGCCTTAt                                                                        <  2:788070/139‑1 (MQ=255)
                                      aCCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAACCGCCTTATCCGGCCTa                                                                >  1:788070/1‑139 (MQ=18)
                                            gCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATg                                                          <  2:532747/139‑1 (MQ=14)
                                              cGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGt                                                        >  1:573370/1‑139 (MQ=17)
                                                    cggcgTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGa                                                  <  2:573370/139‑1 (MQ=17)
                                                                              ggAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAg                                          >  1:616118/1‑121 (MQ=17)
                                                                              ggAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAg                                          <  2:616118/121‑1 (MQ=18)
                                                                                       gggAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCAt               <  1:574579/139‑1 (MQ=18)
                                                                                       gggAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCAt               >  2:574579/1‑139 (MQ=17)
                                                                                          aaTTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAg            >  1:802165/1‑139 (MQ=17)
                                                                                          aaTTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAg            <  2:802165/139‑1 (MQ=18)
                                                                                          aaTTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAg            <  2:769545/139‑1 (MQ=17)
                                                                                                    ccTGATAAGACGCGCAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTTGGCa  <  2:644191/139‑1 (MQ=255)
                                                                                                                  cAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCggg                                                   <  2:372141/76‑1 (MQ=255)
                                                                                                                  cAAGCGTCGCATCGGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCggg                                                   >  1:372141/1‑76 (MQ=19)
                                                                                                                               |                                                                                                               
CCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTCGGCACCATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGAGGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTCGGCACCGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGGATGGTGCGGGAATTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCAGTTGGCA  >  NC_000913/4325907‑4326145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A