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 I1 R1 81 28.9 1316934 95.8% 1261622 113.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,967,135 (C)5→6 coding (303/390 nt) cheY ← chemotaxis regulator transmitting signal to flagellar motor component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,967,1301.C100.0% 56.6 / NA 16A103G (GCC→GGC) cheYchemotaxis regulator transmitting signal to flagellar motor component
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (6/10);  total (6/10)

CCAGCTGAATGCTCGTCAGCAGGTTTGATTGATGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGG‑CCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATCGCGCCATCCGCACGAATTGTTTTCAGCAATTCCAGGCCAT  >  NC_000913/1966994‑1967247
                                                                                                                                         |                                                                                                                     
ccAGCTGAATGCTCGTCAGCAGGTTTGATTGATGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGG‑cc                                                                                                                     >  2:165078/1‑139 (MQ=255)
ccAGCTGAATGCTCGTCAGCAGGTTTGATTGATGGTTGCATCATAGTCGCATACTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGATAAATGGCTTCACCACATAGCCACTGG‑cc                                                                                                                     >  2:445329/1‑139 (MQ=255)
 cAGCTGAATGCTCGTCAGCAGGTTTGATTGATGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGG‑ccc                                                                                                                    <  1:21776/139‑1 (MQ=255)
            tCGTCAGCAGGTTTGATTGATGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTgcgc                                                                                                          <  2:80186/139‑1 (MQ=255)
                       tttGATTGATGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAatga                                                                                               <  1:14952/139‑1 (MQ=255)
                             tgatGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTtct                                                                                         <  2:276971/139‑1 (MQ=255)
                                              tCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCa                                                                        >  1:307394/1‑139 (MQ=255)
                                               cGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAg                                                                       <  1:165078/139‑1 (MQ=255)
                                                 cATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTc                                                                     >  1:48982/1‑139 (MQ=255)
                                                 cATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTc                                                                     >  1:422034/1‑139 (MQ=255)
                                                   tCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTctct                                                                                       <  2:199456/119‑1 (MQ=255)
                                                   tCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTctct                                                                                       >  1:199456/1‑119 (MQ=255)
                                                              ccAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCAtt                                                               <  1:635688/132‑1 (MQ=255)
                                                              ccAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCAtt                                                               >  2:635688/1‑132 (MQ=255)
                                                                               ttgttgAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATcgcg                                       <  1:445329/139‑1 (MQ=255)
                                                                                                      cgcgGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATCGCGCCATCCGCACGAATTGTTTTCAg                <  2:422034/139‑1 (MQ=255)
                                                                                                      cgcgGCGGTAAATGGCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATCGCGCCATCCGCACGAATTGTTTTCAg                <  2:48982/139‑1 (MQ=255)
                                                                                                                    gCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATCGCGCCATCCGCACGAATTGTTTTCAGCAATTCCAGGccgt  <  2:307394/139‑3 (MQ=255)
                                                                                                                    gCTTCACCACATAGCCACTGGCCCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATCGCGCCATCCGCACGAATTGTTTTCAGCAATTCCAGGccat  >  1:275351/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                     
CCAGCTGAATGCTCGTCAGCAGGTTTGATTGATGGTTGCATCATAGTCGCATCCTCACATGCCCAGTTTCTCAAAGATTTTGTTGAGTTTTTCCTCCAGCGTCGCGGCGGTAAATGGCTTCACCACATAGCCACTGG‑CCCCCGCTTGCGCCGCAGCAATGATGTTCTCTTTCTTCGCTTCTGCAGTCACCATTAACACTGGCAATGCCGACATCGCGCCATCCGCACGAATTGTTTTCAGCAATTCCAGGCCAT  >  NC_000913/1966994‑1967247

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A