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
A1 F169 I1 R1 62 44.4 970160 98.1% 951726 147.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,079,114 T→C H201R (CAC→CGC)  natA_1 ← ABC transporter ATP‑binding protein NatA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,079,1140TC100.0% 87.4 / NA 25H201R (CAC→CGC) natA_1ABC transporter ATP‑binding protein NatA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/15);  total (10/15)

AAATCCCGTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAGTAGGCTC  >  USA300TCH1516_ALE/2078972‑2079256
                                                                                                                                              |                                                                                                                                              
aaaTCCCGTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATg                                                                                                                                           >  3:71099/1‑148 (MQ=255)
             ttATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTa                                                                                                                              >  4:381433/1‑148 (MQ=255)
                   tcttcATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTAtttttt                                                                                                                        >  4:182866/1‑148 (MQ=255)
                                 tAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATa                                                                                                          >  4:259695/1‑148 (MQ=255)
                                             ttCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGAc                                                                                              >  3:260007/1‑148 (MQ=255)
                                              tcatcatcaAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAAtgtgt                                                                                                    >  2:18756/1‑141 (MQ=255)
                                                                 tAGCCCCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTATATTTtc                                                                          <  3:395163/148‑1 (MQ=255)
                                                                 tAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTTAGATAATGTGTGTCGACATGAATATTGTTTTATTTtc                                                                          <  4:374043/148‑1 (MQ=255)
                                                                 tAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTtc                                                                          <  3:209210/148‑1 (MQ=255)
                                                                      ccacTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTATATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCaa                                                                     >  4:265175/1‑148 (MQ=255)
                                                                               aCTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCtt                                                            <  3:182866/148‑1 (MQ=255)
                                                                                cTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTg                                                           >  4:353922/1‑148 (MQ=255)
                                                                                                cAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAAt                                           <  3:49537/148‑1 (MQ=255)
                                                                                                  gttgttCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAg                                         <  4:395140/148‑1 (MQ=255)
                                                                                                  gttgttCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAg                                         <  4:222248/148‑1 (MQ=255)
                                                                                                  gttgttCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAg                                         <  4:26103/148‑1 (MQ=255)
                                                                                                                ccATTTAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTTTTTTTCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTAATCAATTAATTATTGCTGAATTATATCCAATAGCTCATTTTTAGcaa                           >  4:15863/1‑146 (MQ=255)
                                                                                                                     tAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGa                      <  4:236498/148‑1 (MQ=255)
                                                                                                                     tAAGATAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGa                      <  3:149478/148‑1 (MQ=255)
                                                                                                                         aTAACTTCACCGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCaa                  >  3:179217/1‑148 (MQ=255)
                                                                                                                                  ccGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAg         <  4:11379/148‑1 (MQ=255)
                                                                                                                                  ccGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAg         <  4:391294/148‑1 (MQ=255)
                                                                                                                                  ccGTCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAg         <  4:398263/148‑1 (MQ=255)
                                                                                                                                     tCACTTAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCt             <  2:11179/141‑1 (MQ=255)
                                                                                                                                         ttAAGCGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAGTAGGCtc  <  3:122179/148‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                              
AAATCCCGTACGCTTATGTTCTTCATAAATAAGTAGAGATGCTAATTCATCATCAAGGTCCTCAATAGCACCACTCACAACTTGATATCTTTGTAACAGTTGTTCTTTTGAACCATTTAAGATAACTTCACCGTCACTTAAGTGAATGATATAATCAGCTATTTTTTCTAAATCTGAGATAATGTGTGTCGACATGAATATTGTTTTATTTTCATCAATTAATTCTTGCTGAATTATCTCCAATAGCTCATTTCTAGCTAAGGGATCAAGACCTGAAGTAGGCTC  >  USA300TCH1516_ALE/2078972‑2079256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A